Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 118 of 311
Found at i:39295182 original size:40 final size:40
Alignment explanation
Indices: 39295127--39295209 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
39295117 CATATATGTG
* *
39295127 ATAAGGCCGAATGGCCAATGCGATGAATGTGAGCATGCAT
1 ATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCAT
*
39295167 ATAAGGCCGAATGGCCAATGTGATGAATATGAACATGCAT
1 ATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCAT
39295207 ATA
1 ATA
39295210 TGTGGTAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (40 bp):
ATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCAT
Found at i:39295551 original size:37 final size:37
Alignment explanation
Indices: 39295443--39295551 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
39295433 GGAAATATAT
*
39295443 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
39295480 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
39295517 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
39295552 CGTCTGATGT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:39300575 original size:29 final size:29
Alignment explanation
Indices: 39300497--39300575 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
39300487 GCATGTATAA
* *
39300497 GAATGTGATTTGGGCCTAATAGGCCATAT
1 GAATGTGATTTGGGCCTAATGGGCCAAAT
39300526 GAATGTGATTTGGGCCTAATGGGCCAAAT
1 GAATGTGATTTGGGCCTAATGGGCCAAAT
39300555 GAATGTGATTTGGGCCTAATG
1 GAATGTGATTTGGGCCTAATG
39300576 TGTGACAGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (29 bp):
GAATGTGATTTGGGCCTAATGGGCCAAAT
Found at i:39302286 original size:40 final size:40
Alignment explanation
Indices: 39302228--39302412 Score: 282
Period size: 40 Copynumber: 4.6 Consensus size: 40
39302218 CGGATGATAA
* * *
39302228 CCGGGCTAAGTCCCGAAGGCATTTGTTCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
39302268 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
**
39302308 CCAAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39302348 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39302388 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
39302413 AGCAAGTAGT
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 132 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39302427 original size:80 final size:79
Alignment explanation
Indices: 39302224--39302444 Score: 266
Period size: 80 Copynumber: 2.8 Consensus size: 79
39302214 TATTCGGATG
* * * *
39302224 ATAACCGGGCTAAGTCCCGAAGGCATTTGTTCTAGTGACTA-ATTCCGGGCTAAGTCCTGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ATTATA-TCCGGGCTAAGTCCCGAAGGC
39302288 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTTACT
* ** * *
39302304 ATATCCAAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TATTATATCCGGGCTAAGTCCCGAAGGCA
*
39302369 TTTGTGTGAGTTACT
65 TTTGTGCGAGTTACT
* * * *
39302384 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGTTATATTC-AGCTAAATCCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTA-TTATATCCGGGCTAAGTCCCGAAG
39302445 ATGCTTGGGT
Statistics
Matches: 122, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
79 15 0.12
80 105 0.86
81 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTATTATATCCGGGCTAAGTCCCGAAGGCAT
TTGTGCGAGTTACT
Found at i:39302712 original size:22 final size:21
Alignment explanation
Indices: 39302671--39302714 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
39302661 GAATGTGCAT
39302671 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
39302693 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
39302715 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:39310289 original size:40 final size:40
Alignment explanation
Indices: 39310232--39310416 Score: 300
Period size: 40 Copynumber: 4.6 Consensus size: 40
39310222 CGGATGATAA
* * *
39310232 CCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
39310272 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
**
39310312 CCAAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39310352 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39310392 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
39310417 AGCAAGTAGT
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
40 135 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39310431 original size:80 final size:79
Alignment explanation
Indices: 39310228--39310448 Score: 293
Period size: 80 Copynumber: 2.8 Consensus size: 79
39310218 TATTCGGATG
* * *
39310228 ATAACCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ATTATA-TCCGGGCTAAGTCCCGAAGGC
39310292 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTTACT
* ** * *
39310308 ATATCCAAGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TATTATATCCGGGCTAAGTCCCGAAGGCA
39310373 TTTGTGCGAGTTACT
65 TTTGTGCGAGTTACT
* * *
39310388 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGTTATATTC-GGCTAAATCCCGAAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTA-TTATATCCGGGCTAAGTCCCGAAG
39310449 ATGCTTGGGT
Statistics
Matches: 125, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
79 16 0.13
80 107 0.86
81 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTATTATATCCGGGCTAAGTCCCGAAGGCAT
TTGTGCGAGTTACT
Found at i:39310716 original size:22 final size:21
Alignment explanation
Indices: 39310675--39310718 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
39310665 GAATGTGCAT
39310675 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
39310697 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
39310719 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:39311866 original size:28 final size:29
Alignment explanation
Indices: 39311803--39311870 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
39311793 GGGTGTTACA
* **
39311803 TAATGGGCCAAATGAATGTGATTTGGGCC
1 TAATGGGCCATATGAATAAGATTTGGGCC
*
39311832 TAATGGGCCATATGAATAAG-TTTGGGCT
1 TAATGGGCCATATGAATAAGATTTGGGCC
*
39311860 TAGTGGGCCAT
1 TAATGGGCCAT
39311871 GTGCATGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 17 0.50
29 17 0.50
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.29
Consensus pattern (29 bp):
TAATGGGCCATATGAATAAGATTTGGGCC
Found at i:39316524 original size:23 final size:22
Alignment explanation
Indices: 39316493--39316535 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
39316483 TTATGAATCA
* *
39316493 TATGTTTTGGTATGATGTTGGCT
1 TATGATTTGGCATGAT-TTGGCT
39316516 TATGATTTGGCATGATTTGG
1 TATGATTTGGCATGATTTGG
39316536 TATGTATTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.16, C:0.05, G:0.30, T:0.49
Consensus pattern (22 bp):
TATGATTTGGCATGATTTGGCT
Found at i:39332645 original size:44 final size:43
Alignment explanation
Indices: 39332575--39332779 Score: 209
Period size: 44 Copynumber: 4.7 Consensus size: 43
39332565 TATGTGTTAT
*
39332575 CGTGTAAGACCATGTTTGGGACGTTGGCATCGACTTATGATTTA
1 CGTGTAAGACCACGTTT-GGACGTTGGCATCGACTTATGATTTA
* * *
39332619 CATGTAAGACCACATTTAGGATGTTGGCATCGACTTATGATTTA
1 CGTGTAAGACCACGTTT-GGACGTTGGCATCGACTTATGATTTA
* * *
39332663 CGTGTAAGACCATGTCTTGGACCTTGGCATCGACGTATGATTTA
1 CGTGTAAGACCACGT-TTGGACGTTGGCATCGACTTATGATTTA
* * * *
39332707 TGTGTAAGACCACGTCTGGGACAG-TGGTATCGA-TATTTGA-TTA
1 CGTGTAAGACCACGT-TTGGAC-GTTGGCATCGACT-TATGATTTA
* *
39332750 CATGTAAGACCACGATTGGGACGTTGGCAT
1 CGTGTAAGACCACG-TTTGGACGTTGGCAT
39332780 TGTACTAGTT
Statistics
Matches: 135, Mismatches: 21, Indels: 11
0.81 0.13 0.07
Matches are distributed among these distances:
42 1 0.01
43 26 0.19
44 106 0.79
45 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCACGTTTGGACGTTGGCATCGACTTATGATTTA
Found at i:39333652 original size:21 final size:23
Alignment explanation
Indices: 39333607--39333655 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
39333597 ATGATGTCTG
*
39333607 ATTTGGTTGTAAAATGGTTGAGA
1 ATTTGGTTATAAAATGGTTGAGA
*
39333630 ATTTGG-TATAAAAT-GTTGTGA
1 ATTTGGTTATAAAATGGTTGAGA
39333651 ATTTG
1 ATTTG
39333656 TTGCTTGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 7 0.29
23 6 0.25
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.43
Consensus pattern (23 bp):
ATTTGGTTATAAAATGGTTGAGA
Found at i:39340412 original size:43 final size:43
Alignment explanation
Indices: 39340287--39340441 Score: 190
Period size: 43 Copynumber: 3.6 Consensus size: 43
39340277 ATGTGTTACC
* * * *
39340287 GTGTAAGACCACGTCTAGGACGTTGGAATCGACATATGATTTAT
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTT-T
*
39340331 GTGTAAGACCACGTCTGGGACGTTGGCATCG-TACTTGATTTT
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTT
**
39340373 GTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGATTAC
1 GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTTT
*
39340416 ATGTAAGACCACGTCTGGGACGTTGG
1 GTGTAAGACCACGTCTGGGACGTTGG
39340442 AATTGTACGA
Statistics
Matches: 97, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
41 1 0.01
42 29 0.30
43 37 0.38
44 30 0.31
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTT
Found at i:39341293 original size:21 final size:23
Alignment explanation
Indices: 39341248--39341296 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
39341238 ATGATGTATG
*
39341248 ATTTGGTTGTAAAATGGTTGAGA
1 ATTTGGTTATAAAATGGTTGAGA
*
39341271 ATTTGG-TATAAAAT-GTTGTGA
1 ATTTGGTTATAAAATGGTTGAGA
39341292 ATTTG
1 ATTTG
39341297 TTGTTAGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 7 0.29
23 6 0.25
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.43
Consensus pattern (23 bp):
ATTTGGTTATAAAATGGTTGAGA
Found at i:39342915 original size:58 final size:57
Alignment explanation
Indices: 39342776--39342916 Score: 144
Period size: 57 Copynumber: 2.5 Consensus size: 57
39342766 ATGTATACAA
** ** *
39342776 CAGGATTACCAGT-TCAGGCTAAATCCTTTTTATGACATATGCTCTAAAGAGCTTAAT
1 CAGGATTACCAGTCT-AGGCTAAATCCAGTCAATAACATATGCTCTAAAGAGCTTAAT
* * **
39342833 CTGGATTACCTGTCCGGGCTAAATCCAGTCAATAACATATGCT-TGAAAG-GACTTAGAT
1 CAGGATTACCAGTCTAGGCTAAATCCAGTCAATAACATATGCTCT-AAAGAG-CTTA-AT
39342891 CAGGATTACCAGTCTAGGCTAAATCC
1 CAGGATTACCAGTCTAGGCTAAATCC
39342917 TTTCTGTAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
56 2 0.03
57 41 0.61
58 24 0.36
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (57 bp):
CAGGATTACCAGTCTAGGCTAAATCCAGTCAATAACATATGCTCTAAAGAGCTTAAT
Found at i:39352832 original size:22 final size:22
Alignment explanation
Indices: 39352804--39352849 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
39352794 ACGCCGTAGG
*
39352804 CAGGACAACACATAGCCTTAAA
1 CAGGACAACACATAGCCGTAAA
*
39352826 CAGGACAGCACATAGCCGTAAA
1 CAGGACAACACATAGCCGTAAA
39352848 CA
1 CA
39352850 TCGCAGCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.28, G:0.17, T:0.11
Consensus pattern (22 bp):
CAGGACAACACATAGCCGTAAA
Found at i:39352856 original size:22 final size:22
Alignment explanation
Indices: 39352807--39352857 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
39352797 CCGTAGGCAG
* * *
39352807 GACAACACATAGCCTTAAACAG
1 GACAGCACATAGCCGTAAACAC
39352829 GACAGCACATAGCCGTAAACATC
1 GACAGCACATAGCCGTAAACA-C
39352852 G-CAGCA
1 GACAGCA
39352858 ACACTGCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.12
Consensus pattern (22 bp):
GACAGCACATAGCCGTAAACAC
Found at i:39353337 original size:41 final size:41
Alignment explanation
Indices: 39353258--39353416 Score: 239
Period size: 41 Copynumber: 3.9 Consensus size: 41
39353248 TAAAAGCCAC
*
39353258 CGGTGGATCCACGGTCGTCAAG-AACCATGCGATCCTTAAT
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTTAAT
* * * *
39353298 CGGTGGATCCACGGTCGTTAAGAAACCATGTGATCCTTAAT
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTTAAT
* *
39353339 CGGTGGATCCACGATTGTCAAGCAACCATGCGATCCTCAAT
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTTAAT
*
39353380 CGGTGGATCCACAATCGTCAAGCAACCATGCGATCCT
1 CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCT
39353417 CAATTTCTTC
Statistics
Matches: 108, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 21 0.19
41 87 0.81
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (41 bp):
CGGTGGATCCACGATCGTCAAGCAACCATGCGATCCTTAAT
Found at i:39353710 original size:27 final size:27
Alignment explanation
Indices: 39353666--39354054 Score: 264
Period size: 27 Copynumber: 14.4 Consensus size: 27
39353656 TACAAGGGGG
* * *
39353666 TTTTGGTAAATCTACAAACCAAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * *
39353693 TTTTGGTAATTTTGCAAACCAATGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* **
39353720 TTTTTGTAATTTTTGAAAGTCAAGGGTA
1 TTTTGGTAATTTTACAAA-TCAAGGGTA
* ** *
39353748 TTTTTGTAATTTTGTAAATCAGGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * *
39353775 TTTCT-ATAACTTTCCAAATCAAGGGTA
1 TTT-TGGTAATTTTACAAATCAAGGGTA
* * * * *
39353802 TTTCGATAATTTTCCAAATTAGGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* *
39353829 TTTTGGTAATTTTACAAATTGAA-AGTA
1 TTTTGGTAATTTTACAAA-TCAAGGGTA
*
39353856 TTTTGGTAATTTTACAAGTCGAA-GGTA
1 TTTTGGTAATTTTACAAATC-AAGGGTA
* ** * *
39353883 TTTCGGTAATTTTACAGGTCGAGAGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * **
39353910 TTTCGGTAATTTCACAAATCTGGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * *
39353937 TTTTGGTGATTTTACAAACCAAGGTTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
* * * *
39353964 TTTTGGTAATTTTGCTAATCGATGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
** *
39353991 TTTTGGTAATTTTGTAAACCAAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
** ** * *
39354018 -TTCAGTAATTTTGTAAACCACGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
*
39354044 TTTTAGTAATT
1 TTTTGGTAATT
39354055 CTACCCTACA
Statistics
Matches: 292, Mismatches: 63, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
26 25 0.09
27 241 0.83
28 26 0.09
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.41
Consensus pattern (27 bp):
TTTTGGTAATTTTACAAATCAAGGGTA
Found at i:39353812 original size:54 final size:53
Alignment explanation
Indices: 39353680--39353831 Score: 151
Period size: 55 Copynumber: 2.8 Consensus size: 53
39353670 GGTAAATCTA
* * ** * * * *
39353680 CAAACCAAGGGTATTTTGGTAATTTTGCAAACCAATGGTATTTTTGTAATTTTT
1 CAAATCAAGGGTATTTT-GTAATTTTGCAAATCAGGGGTATTTCTATAACTTTC
* *
39353734 GAAAGTCAAGGGTATTTTTGTAATTTTGTAAATCAGGGGTATTTCTATAACTTTC
1 CAAA-TCAAGGGTA-TTTTGTAATTTTGCAAATCAGGGGTATTTCTATAACTTTC
* * *
39353789 CAAATCAAGGGTATTTCGATAATTTTCCAAATTAGGGGTATTT
1 CAAATCAAGGGTATTTTG-TAATTTTGCAAATCAGGGGTATTT
39353832 TGGTAATTTT
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
53 4 0.05
54 33 0.41
55 39 0.49
56 4 0.05
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (53 bp):
CAAATCAAGGGTATTTTGTAATTTTGCAAATCAGGGGTATTTCTATAACTTTC
Found at i:39354069 original size:27 final size:27
Alignment explanation
Indices: 39354039--39354092 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39354029 TGTAAACCAC
* * *
39354039 GGGTATTTTAGTAATTCTACCCTACAG
1 GGGTATTTCAATAATACTACCCTACAG
*
39354066 GGGTATTTCAATAATACTAGCCTACAG
1 GGGTATTTCAATAATACTACCCTACAG
39354093 ATATGAGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
GGGTATTTCAATAATACTACCCTACAG
Found at i:39374709 original size:30 final size:30
Alignment explanation
Indices: 39374675--39374734 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
39374665 CTTTAATACG
39374675 AACTTTAGAAAAATTACA-TTTTTGCCCCTA
1 AACTTTAGAAAAATTACACTTTTT-CCCCTA
* * *
39374705 AACTTTTGCATAATTACACTTTTTCCCCTA
1 AACTTTAGAAAAATTACACTTTTTCCCCTA
39374735 GGCTCGGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (30 bp):
AACTTTAGAAAAATTACACTTTTTCCCCTA
Found at i:39382507 original size:16 final size:16
Alignment explanation
Indices: 39382486--39382518 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39382476 GGTATGGATT
39382486 GCTGATAAGAGTGTCA
1 GCTGATAAGAGTGTCA
39382502 GCTGATAAGAGTGTCA
1 GCTGATAAGAGTGTCA
39382518 G
1 G
39382519 TCCTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.24
Consensus pattern (16 bp):
GCTGATAAGAGTGTCA
Found at i:39386790 original size:42 final size:39
Alignment explanation
Indices: 39386729--39386816 Score: 149
Period size: 42 Copynumber: 2.2 Consensus size: 39
39386719 TGCTTTTCAT
39386729 ATAAAAAATATTTAAAAATTAAAATCCATAAATAAATAA
1 ATAAAAAATATTTAAAAATTAAAATCCATAAATAAATAA
39386768 ATAAATAAATATTTCTAAAAATTAAAATCCATAAATAAATAA
1 ATAAA-AAATA-TT-TAAAAATTAAAATCCATAAATAAATAA
39386810 ATAAAAA
1 ATAAAAA
39386817 TTTCTAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
39 5 0.11
40 5 0.11
41 4 0.09
42 32 0.70
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (39 bp):
ATAAAAAATATTTAAAAATTAAAATCCATAAATAAATAA
Found at i:39386811 original size:38 final size:39
Alignment explanation
Indices: 39386729--39386829 Score: 129
Period size: 38 Copynumber: 2.6 Consensus size: 39
39386719 TGCTTTTCAT
39386729 ATAAA-AAATA-TT-TAAAAATTAAAATCCATAAATAAATAA
1 ATAAATAAATATTTCTAAAAATTAAAATCC---AATAAATAA
39386768 ATAAATAAATATTTCTAAAAATTAAAATCC-ATAAATAA
1 ATAAATAAATATTTCTAAAAATTAAAATCCAATAAATAA
* *
39386806 ATAAATAAAAATTTCTAATAATTA
1 ATAAATAAATATTTCTAAAAATTA
39386830 TTTAAAAACC
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
38 30 0.53
39 5 0.09
40 5 0.09
41 2 0.04
42 15 0.26
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (39 bp):
ATAAATAAATATTTCTAAAAATTAAAATCCAATAAATAA
Found at i:39386842 original size:42 final size:38
Alignment explanation
Indices: 39386732--39386829 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 38
39386722 TTTTCATATA
*
39386732 AAAAATATT-TAAAAATTAAAATCCATAAATAAATAAAT
1 AAAAAT-TTCTAAAAATTAAAAACCATAAATAAATAAAT
*
39386770 AAATAAATATTTCTAAAAATTAAAATCCATAAATAAATAAAT
1 --A-AAA-ATTTCTAAAAATTAAAAACCATAAATAAATAAAT
*
39386812 AAAAATTTCTAATAATTA
1 AAAAATTTCTAAAAATTA
39386830 TTTAAAAACC
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
38 13 0.24
39 3 0.06
40 2 0.04
41 5 0.09
42 31 0.57
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (38 bp):
AAAAATTTCTAAAAATTAAAAACCATAAATAAATAAAT
Found at i:39387351 original size:10 final size:10
Alignment explanation
Indices: 39387336--39387407 Score: 55
Period size: 10 Copynumber: 7.7 Consensus size: 10
39387326 ATTTGTAATG
39387336 ATTATTTATA
1 ATTATTTATA
39387346 ATTATTTATA
1 ATTATTTATA
* *
39387356 ATTCTTAATA
1 ATTATTTATA
39387366 ATT-TTTA-A
1 ATTATTTATA
**
39387374 AGAATTTATA
1 ATTATTTATA
*
39387384 ATT-TTTTTA
1 ATTATTTATA
*
39387393 A-AATTT-TA
1 ATTATTTATA
39387401 ATTATTT
1 ATTATTT
39387408 GAAAAACCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
8 5 0.10
9 20 0.42
10 23 0.48
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (10 bp):
ATTATTTATA
Found at i:39387397 original size:18 final size:19
Alignment explanation
Indices: 39387363--39387403 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
39387353 ATAATTCTTA
39387363 ATAA-TTTTTAAAGAATTT
1 ATAATTTTTTAAAGAATTT
*
39387381 ATAATTTTTTTAA-AATTT
1 ATAATTTTTTAAAGAATTT
39387399 -TAATT
1 ATAATT
39387404 ATTTGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 9 0.43
19 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATAATTTTTTAAAGAATTT
Found at i:39387412 original size:17 final size:18
Alignment explanation
Indices: 39387339--39387412 Score: 55
Period size: 19 Copynumber: 4.1 Consensus size: 18
39387329 TGTAATGATT
39387339 ATTTATAATTATTT-ATAA
1 ATTTATAATTATTTGA-AA
* *
39387357 TTCTTAATAATT-TTTAAAGA
1 AT-TT-ATAATTATTTGAA-A
* *
39387377 ATTTATAATTTTTTTAAA
1 ATTTATAATTATTTGAAA
39387395 ATTT-TAATTATTTGAAA
1 ATTTATAATTATTTGAAA
39387412 A
1 A
39387413 ACCTTGTCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
17 12 0.26
18 12 0.26
19 13 0.28
20 9 0.20
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTATAATTATTTGAAA
Found at i:39387509 original size:7 final size:7
Alignment explanation
Indices: 39387497--39387540 Score: 61
Period size: 7 Copynumber: 6.0 Consensus size: 7
39387487 AATTACAGAA
39387497 ATTTTTT
1 ATTTTTT
39387504 ATTTTTT
1 ATTTTTT
39387511 ATTTTTT
1 ATTTTTT
*
39387518 TTTGGTTTT
1 ATT--TTTT
39387527 ATTTTTT
1 ATTTTTT
39387534 ATTTTTT
1 ATTTTTT
39387541 TAAATAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 27 0.82
9 6 0.18
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (7 bp):
ATTTTTT
Found at i:39390255 original size:46 final size:45
Alignment explanation
Indices: 39390152--39390322 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 45
39390142 TTGTGTGAGC
* * *
39390152 TAGTGTAAGACATGTCTGGGACATGTCATCAGCATTGAGACG-AGTG
1 TAGTGTAAGACATGTCTGGGACATG-CATCGGCCTCGAGACGTAG-G
* *
39390198 CTAGTGTAAGACATGTCTAGGACATGCTTCGGCCTCGAGACGTAAGG
1 -TAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGT-AGG
*
39390245 TAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGT--G
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGTAGG
39390288 TCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 T-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
39390323 ACCTGACCCC
Statistics
Matches: 109, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
43 2 0.02
44 9 0.08
45 16 0.15
46 55 0.50
47 25 0.23
48 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (45 bp):
TAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAGG
Found at i:39397710 original size:12 final size:12
Alignment explanation
Indices: 39397693--39397726 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39397683 TATTGTTATA
39397693 ATCTATTTATCT
1 ATCTATTTATCT
*
39397705 ATCTATCTATCT
1 ATCTATTTATCT
*
39397717 ATTTATTTAT
1 ATCTATTTAT
39397727 TTGTTCTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (12 bp):
ATCTATTTATCT
Found at i:39399693 original size:19 final size:19
Alignment explanation
Indices: 39399669--39399713 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
39399659 CGTCTCTTTT
39399669 TGCATT-CATTTCATGCATA
1 TGCATTGCATTTCAT-CATA
39399688 TGCATTGCATTTCATCATA
1 TGCATTGCATTTCATCATA
39399707 TGCATTG
1 TGCATTG
39399714 AATGTCACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.42
Consensus pattern (19 bp):
TGCATTGCATTTCATCATA
Found at i:39402405 original size:43 final size:42
Alignment explanation
Indices: 39402281--39402445 Score: 140
Period size: 43 Copynumber: 3.9 Consensus size: 42
39402271 CAATGTCAAC
* * * * *
39402281 GTCCCAGGCGTGGTCTTACATGTAATCACATGTCGATGCCACT
1 GTCCCAGACATGGTCTTACACGAAATCACATATCGATGCCA-T
* *
39402324 ATCCCAGACAGGGTCTTACACG-AATCACAATTAT-GATGCCGAT
1 GTCCCAGACATGGTCTTACACGAAATCAC-A-TATCGATGCC-AT
* *
39402367 GTCCCAAACATGGTCTTACTA-GAAATCACATATCGATGCCAAC
1 GTCCCAGACATGGTCTTAC-ACGAAATCACATATCGATGCC-AT
* *
39402410 GTCCTAGACGTGGTCTTACACGAGAA-CACATATCGA
1 GTCCCAGACATGGTCTTACACGA-AATCACATATCGA
39402446 AAATCCTATG
Statistics
Matches: 100, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
42 10 0.10
43 78 0.78
44 12 0.12
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGAAATCACATATCGATGCCAT
Found at i:39408591 original size:39 final size:40
Alignment explanation
Indices: 39408547--39408710 Score: 219
Period size: 40 Copynumber: 4.2 Consensus size: 40
39408537 CCTTCGAAAT
* * *
39408547 TTAG-CCGGATATAGCT-ACTTGCTCAAATCCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
*
39408586 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
*
39408626 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAG-C
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
39408665 TTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGAC
39408705 TTAGCC
1 TTAGCC
39408711 TGGTTATCAT
Statistics
Matches: 112, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 39 0.35
40 72 0.64
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:39408672 original size:79 final size:80
Alignment explanation
Indices: 39408547--39408710 Score: 219
Period size: 79 Copynumber: 2.1 Consensus size: 80
39408537 CCTTCGAAAT
* * * * *
39408547 TTAG-CCGGATATAGCTACTTGCTCAAATCCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
1 TTAGCCCGGATATAGCTACTCGCACAAATCCCTTCGAGACTTAGCCCGGAAT-TAGTAACTAGCA
39408610 CAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
* *
39408626 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGAG-CTTAGCCCGGAATTAGTCACTAGCA
1 TTAGCCCGGATATAGCT-ACTCGCACAAATCCCTTCGAGACTTAGCCCGGAATTAGTAACTAGCA
39408689 CAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
39408705 TTAGCC
1 TTAGCC
39408711 TGGTTATCAT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
79 47 0.63
80 28 0.37
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATATAGCTACTCGCACAAATCCCTTCGAGACTTAGCCCGGAATTAGTAACTAGCAC
AAATGCCTTCGGGAC
Found at i:39410325 original size:47 final size:47
Alignment explanation
Indices: 39410246--39410564 Score: 512
Period size: 47 Copynumber: 6.7 Consensus size: 47
39410236 CCCTTCGGGA
* * * * * * *
39410246 CTTATCACATTTATACACTTTCACATCCATCACGTTGGTCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
39410293 CCTGTCACATATATACACTTTCACATTTATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39410340 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39410389 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39410436 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39410483 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39410530 CTTATCACATATATACACTTTCACATCCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
39410565 AGAATCCTAA
Statistics
Matches: 254, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
47 209 0.82
49 45 0.18
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39410544 original size:143 final size:142
Alignment explanation
Indices: 39410246--39410564 Score: 523
Period size: 143 Copynumber: 2.2 Consensus size: 142
39410236 CCCTTCGGGA
* * * * * *
39410246 CTTATCACATTTATACACTTTCACATCCATCACGTTGGTCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
* *
39410311 TTTCACATTTATCACATCGGCTATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATACACTTTCACATTCATCACA
39410376 TCGGCCATTAGGC
130 TCGGCCATTAGGC
* * *
39410389 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
39410454 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATACACTTTCACATTCATCACAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCACAT
39410518 CGGCCATTAGGC
131 CGGCCATTAGGC
39410530 CTTATCACATATATACACTTTCACATCCATCACAT
1 CTTATCACATATATACACTTTCACATCCATCACAT
39410565 AGAATCCTAA
Statistics
Matches: 164, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
141 73 0.45
143 91 0.55
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (142 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCACAT
CGGCCATTAGGC
Found at i:39414195 original size:40 final size:40
Alignment explanation
Indices: 39413962--39414195 Score: 301
Period size: 40 Copynumber: 5.9 Consensus size: 40
39413952 CGAATACACG
* * * *
39413962 TCACCAGCACGATTGCTCTTCGG-ACCTAGCCCGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
* * ** * *
39414001 ACACCAGCACGAATGCTCTTCGG-GTTTAGCACGGATATA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
* * *
39414040 TCACTAGCACAAATGCTCTTCGGAACTTAGTCTGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
* *
39414080 TCACTAGCACGAATGCTCTTCGGAACTTAGTCTGGATACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
* *
39414120 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGAGACA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
39414160 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGA
1 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGA
39414196 CATCATTCGA
Statistics
Matches: 175, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 53 0.30
40 122 0.70
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:39414538 original size:29 final size:29
Alignment explanation
Indices: 39414499--39414577 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
39414489 CTTAATAATC
*
39414499 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
39414529 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
39414558 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39414578 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:39414654 original size:42 final size:43
Alignment explanation
Indices: 39414559--39414660 Score: 188
Period size: 43 Copynumber: 2.4 Consensus size: 43
39414549 TGCATTTCAA
39414559 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
*
39414602 GCCCGCACACTTAGTGCCAATCTCACAATCGTGAA-ACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
39414644 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
39414661 TAAAACCAAC
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 24 0.41
43 34 0.59
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:39416155 original size:47 final size:47
Alignment explanation
Indices: 39416077--39416629 Score: 919
Period size: 47 Copynumber: 11.7 Consensus size: 47
39416067 CCCTTCGGGA
* * * * * *
39416077 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
39416124 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39416171 CTTATCACATATATATACACTTTTACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39416220 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39416267 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39416314 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39416361 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39416408 CTTATCACATATATACACTTTCACA-TCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39416454 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
39416501 CTTATCACATATATACACTTTCACATTAATCACATCAGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39416548 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39416595 CTTATCACATATATACACTTTCACATCCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
39416630 AGAATCCTAA
Statistics
Matches: 478, Mismatches: 25, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
46 45 0.09
47 388 0.81
49 45 0.09
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39416516 original size:234 final size:236
Alignment explanation
Indices: 39416077--39416629 Score: 921
Period size: 234 Copynumber: 2.3 Consensus size: 236
39416067 CCCTTCGGGA
* * * * * * * *
39416077 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
39416142 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATATACACTTTTACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATACACTTTCACATTCATCACA
39416207 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
130 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
* * *
39416272 CACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
195 CACATATATACACTTTCACATTAATCACATCAGCCATTAGGC
*
39416314 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
39416379 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATATATACACTTTCACA-TCATCACAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCACAT
* *
39416442 CGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATC
131 CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
*
39416507 ACATATATACACTTTCACATTAATCACATCAGCCATTAGGT
196 ACATATATACACTTTCACATTAATCACATCAGCCATTAGGC
39416548 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
39416613 TTTCACATCCATCACAT
66 TTTCACATTCATCACAT
39416630 AGAATCCTAA
Statistics
Matches: 297, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
234 189 0.64
235 16 0.05
237 92 0.31
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (236 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
ACATATATACACTTTCACATTAATCACATCAGCCATTAGGC
Found at i:39419963 original size:39 final size:40
Alignment explanation
Indices: 39419862--39420041 Score: 258
Period size: 41 Copynumber: 4.5 Consensus size: 40
39419852 GATGATAACC
* * *
39419862 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCG
* *
39419901 GGCTAAG-GCCGAAGGCATTTGTGCGAGTTACTA-ATTCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCG
39419939 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCG
* *
39419979 CGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAACCG
1 -GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCG
*
39420020 GGCTAAGTCCCGAAGGGATTTG
1 GGCTAAGTCCCGAAGGCATTTG
39420042 AGCAAGTAGT
Statistics
Matches: 130, Mismatches: 8, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
38 35 0.27
39 32 0.25
40 25 0.19
41 38 0.29
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAATCG
Found at i:39429030 original size:47 final size:47
Alignment explanation
Indices: 39428925--39429476 Score: 894
Period size: 47 Copynumber: 11.7 Consensus size: 47
39428915 TTAGGATTCT
*
39428925 ATGTGATGGATGTGAAAGTGTATATATGTGATAAGG-CTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
39428971 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGACCTAATGGCTG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
39429018 ATGTGATTAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
39429065 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
39429112 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
39429159 ATGTGATGAATGTGAAAGTGTTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCG
*
39429207 ATGCGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
39429254 ATGCGATGAATGTGAAAGTGTATATATGTGATAAGG-CTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
39429300 ATGTGATGAATGTGAAAGTGTATATATGT-ATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
39429346 ATGTGATGAATGTAAAAGTGTTATTATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTG-TA-TATATGTGATAAGGCCTAATGGCCG
* * * * *
39429395 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
39429442 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
39429477 TCCGAAGGGC
Statistics
Matches: 475, Mismatches: 25, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
45 6 0.01
46 101 0.21
47 278 0.59
48 55 0.12
49 35 0.07
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:39430946 original size:43 final size:43
Alignment explanation
Indices: 39430885--39430987 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
39430875 TTGGTTTTTA
39430885 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
*
39430928 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
39430971 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
39430988 TTGAAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
Found at i:39431004 original size:29 final size:29
Alignment explanation
Indices: 39430969--39431042 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
39430959 GTTGTGAGAT
* *
39430969 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
39430998 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
39431027 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
39431043 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:39431452 original size:39 final size:39
Alignment explanation
Indices: 39431358--39431582 Score: 263
Period size: 39 Copynumber: 5.7 Consensus size: 39
39431348 GTCCGGGCTA
* *
39431358 AGTTCCGAAGAGCATTCGTGCTAGTGATGTCTCCGGACT
1 AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCAGACT
39431397 AAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCAGACT
1 -AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCAGACT
39431437 AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCAGGACT
1 AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCA-GACT
* * *
39431477 AAGTTCCGAAGAGCATTTGTGCTAGTGATATATCC-GTGCT
1 -AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCAG-ACT
*** * * * * *
39431517 AAACCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCT
1 AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCAGACT
* * *
39431556 AGGTCCGAAGAGCAATCGTGCTGGTGA
1 AGTTCCGAAGAGCATTCGTGCTAGTGA
39431583 CGTGTATTCG
Statistics
Matches: 165, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 89 0.54
40 44 0.27
41 32 0.19
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (39 bp):
AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCAGACT
Found at i:39431502 original size:80 final size:79
Alignment explanation
Indices: 39431358--39431582 Score: 292
Period size: 80 Copynumber: 2.8 Consensus size: 79
39431348 GTCCGGGCTA
*
39431358 AGTTCCGAAGAGCATTCGTGCTAGTGATGTCTCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
1 AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
*
39431423 GATGTATCCAG-ACT
66 GATATATCC-GTACT
*
39431437 AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCAGGACTAAGTTCCGAAGAGCATTTGTGCTAG
1 AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCC-GGACTAAGTTCCGAAGAGCATTCGTGCTAG
*
39431502 TGATATATCCGTGCT
65 TGATATATCCGTACT
*** * * * * * * *
39431517 AAACCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCT-AGGTCCGAAGAGCAATCGTGCTGGT
1 AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
39431581 GA
66 GA
39431583 CGTGTATTCG
Statistics
Matches: 129, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
78 23 0.18
79 38 0.29
80 68 0.53
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
AGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGT
GATATATCCGTACT
Found at i:39431567 original size:119 final size:120
Alignment explanation
Indices: 39431355--39431582 Score: 316
Period size: 119 Copynumber: 1.9 Consensus size: 120
39431345 GATGTCCGGG
* * **
39431355 CTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTCTCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 CTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGACCCGAAGAGCATTCGTGCT
* * *
39431420 AGTGATGTATCCAGACTAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCAGGA
66 AGTGATATATCCAGACTAGGTCCGAAGAGCAATCGTGCTAGTGATGTATCCAGGA
*
39431475 CTAAGTTCCGAAGAGCATTTGTGCTAGTGATATATCCGTG-CTAA-ACCCGAAGAGCATTCGTGC
1 CTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCG-GACTAAGACCCGAAGAGCATTCGTGC
* * * * *
39431538 TGGTGTTATATCCGGGCTAGGTCCGAAGAGCAATCGTGCTGGTGA
65 TAGTGATATATCCAGACTAGGTCCGAAGAGCAATCGTGCTAGTGA
39431583 CGTGTATTCG
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
119 54 0.57
120 39 0.41
121 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
CTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGGACTAAGACCCGAAGAGCATTCGTGCT
AGTGATATATCCAGACTAGGTCCGAAGAGCAATCGTGCTAGTGATGTATCCAGGA
Found at i:39432925 original size:42 final size:40
Alignment explanation
Indices: 39432860--39432986 Score: 159
Period size: 42 Copynumber: 3.1 Consensus size: 40
39432850 TACACAAAGG
*
39432860 CTCTTCGGAACTTAGTCTGGATACATCACTAGGCACGAATT
1 CTCTTCGGAACTTAGTCTGGATACATCACTA-GCACGAATC
39432901 CTCTTCGGAACTTTAGTCTGGATACATCACTAAGCACGAATGC
1 CTCTTCGGAAC-TTAGTCTGGATACATCACT-AGCACGAAT-C
* * * *
39432944 CTCTTCGTAA-TTAGTCCGGAGACATCA-TAGCACGAATG
1 CTCTTCGGAACTTAGTCTGGATACATCACTAGCACGAATC
39432982 CTCTT
1 CTCTT
39432987 TTCGAACTTA
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
38 5 0.06
39 9 0.12
40 1 0.01
41 26 0.33
42 27 0.35
43 10 0.13
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (40 bp):
CTCTTCGGAACTTAGTCTGGATACATCACTAGCACGAATC
Found at i:39433006 original size:38 final size:40
Alignment explanation
Indices: 39432924--39433009 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 40
39432914 TAGTCTGGAT
*
39432924 ACATCACTAAGCACGAATGCCTCTTCGTAATTAGTCCGGAG
1 ACATCA-TAAGCACGAATGCCTCTTCGTAATTAGTCCCGAG
*
39432965 ACATCAT-AGCACGAATGCTCTTTTCG-AACTTAG-CCCG-G
1 ACATCATAAGCACGAATGC-CTCTTCGTAA-TTAGTCCCGAG
39433003 ACATCAT
1 ACATCAT
39433010 TTCGAATAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
38 8 0.20
39 16 0.39
40 11 0.27
41 6 0.15
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (40 bp):
ACATCATAAGCACGAATGCCTCTTCGTAATTAGTCCCGAG
Found at i:39433434 original size:41 final size:42
Alignment explanation
Indices: 39433370--39433472 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 42
39433360 TGCATTTCAA
39433370 GCCCGCACACTTAGCTGCCAATCTCACAA-CCGTGAA-ACTTATT
1 GCCC-CACACTTAG-TGCCAATCTCACAATCCGTGAACA-TTATT
**
39433413 GCCCCACACTTAGTGCCAATCTCACAATCTTTGAACATTATT
1 GCCCCACACTTAGTGCCAATCTCACAATCCGTGAACATTATT
*
39433455 GCCTCACACGTTAGTGCC
1 GCCCCACAC-TTAGTGCC
39433473 TAAAAAACCA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
41 14 0.26
42 27 0.50
43 13 0.24
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (42 bp):
GCCCCACACTTAGTGCCAATCTCACAATCCGTGAACATTATT
Found at i:39435110 original size:46 final size:47
Alignment explanation
Indices: 39434928--39435429 Score: 779
Period size: 47 Copynumber: 10.7 Consensus size: 47
39434918 CTCGGCCCTG
*
39434928 TCACATATATAACACTTTTCACATTTCATCCACATCGGCTATTAGGCCTATA
1 TCACATATAT-ACAC-TTTCACA-TTCAT-CACATCGGCCATTAGGCCT-TA
*
39434980 TCACATATATTACACTTTTACATTCATTCACATCGGCCATTAGGCCTTA
1 TCACATATA-TACACTTTCACATTCA-TCACATCGGCCATTAGGCCTTA
39435029 TCAACACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 T---CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
39435079 TCACATAT-TACACTTTCACATTCATCGCATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
39435125 TCACATATATACACTTTCACATTCATCGCATCGG-CATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
39435171 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
39435218 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
39435265 TCACATATATACACTTTCACATTCATCACA-CGGCTATTA-GCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* *
39435310 TCACATATATACACTTTCACATTAATCACA---GCCATTAGGTCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
39435354 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
39435400 TCACATATATACACTTTCACA-TCATCACAT
1 TCACATATATACACTTTCACATTCATCACAT
39435430 AGAATCCTAA
Statistics
Matches: 429, Mismatches: 10, Indels: 29
0.92 0.02 0.06
Matches are distributed among these distances:
43 6 0.01
44 34 0.08
45 44 0.10
46 124 0.29
47 129 0.30
49 3 0.01
50 45 0.10
51 22 0.05
52 21 0.05
53 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (47 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:39435141 original size:93 final size:94
Alignment explanation
Indices: 39434928--39435429 Score: 779
Period size: 93 Copynumber: 5.3 Consensus size: 94
39434918 CTCGGCCCTG
*
39434928 TCACATATATAACACTTTTCACATTTCATCCACATCGGCTATTAGGCCTATATCACATATATTAC
1 TCACATATAT-ACAC-TTTCACA-TTCAT-CACATCGGCCATTAGGCCT-TATCACATATA-TAC
*
39434993 ACTTTTACATTCATTCACATCGGCCATTAGGCCTTA
60 ACTTTCACATTCA-TCACATCGGCCATTAGGCCTTA
39435029 TCAACACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT-TACACT
1 T---CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
*
39435093 TTCACATTCATCGCATCGGCCATTAGGCCTTA
63 TTCACATTCATCACATCGGCCATTAGGCCTTA
*
39435125 TCACATATATACACTTTCACATTCATCGCATCGG-CATTAGGCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
39435189 ACATTCATCACATCGGCCATTAGGCCTTA
66 ACATTCATCACATCGGCCATTAGGCCTTA
*
39435218 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
*
39435283 ACATTCATCACA-CGGCTATTA-GCCTTA
66 ACATTCATCACATCGGCCATTAGGCCTTA
* *
39435310 TCACATATATACACTTTCACATTAATCACA---GCCATTAGGTCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
39435372 ACATTCATCACATCGGCCATTAGG-CTTA
66 ACATTCATCACATCGGCCATTAGGCCTTA
39435400 TCACATATATACACTTTCACA-TCATCACAT
1 TCACATATATACACTTTCACATTCATCACAT
39435430 AGAATCCTAA
Statistics
Matches: 380, Mismatches: 13, Indels: 27
0.90 0.03 0.06
Matches are distributed among these distances:
89 49 0.13
90 33 0.09
91 1 0.00
92 55 0.14
93 110 0.29
94 41 0.11
96 22 0.06
97 15 0.04
99 10 0.03
100 18 0.05
101 6 0.02
102 7 0.02
103 4 0.01
104 9 0.02
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.33
Consensus pattern (94 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTTA
Found at i:39444392 original size:40 final size:40
Alignment explanation
Indices: 39444341--39444528 Score: 263
Period size: 40 Copynumber: 4.7 Consensus size: 40
39444331 ACTACTTGCT
* *
39444341 CAAATCCCTTCGGGACTTAGCCCGGTTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
39444381 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
**
39444421 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* ** * *
39444461 CAAATGCCTTC-GGCCTTAGCCC-GAAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
39444500 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
39444529 CATCCGAATA
Statistics
Matches: 133, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
38 2 0.02
39 31 0.23
40 98 0.74
41 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:39446496 original size:19 final size:20
Alignment explanation
Indices: 39446455--39446496 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
39446445 ATGCCGAATT
* *
39446455 AAGAAGGACCTTATGTAGTA
1 AAGAAGGACCTTATCTAGAA
*
39446475 AAGAAGG-CCTTCTCTAGAA
1 AAGAAGGACCTTATCTAGAA
39446494 AAG
1 AAG
39446497 TGTTGATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (20 bp):
AAGAAGGACCTTATCTAGAA
Found at i:39446594 original size:3 final size:3
Alignment explanation
Indices: 39446575--39446614 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
39446565 TTTTCCAAAA
* *
39446575 AAG AA- AAG AAT AAG AAG AAG ACG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
39446615 TAAATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.68, C:0.03, G:0.28, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:39446643 original size:12 final size:13
Alignment explanation
Indices: 39446573--39446640 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 13
39446563 AGTTTTCCAA
39446573 AAAAGAAAAGAAT
1 AAAAGAAAAGAAT
* *
39446586 AAGAAGAAGACGAAG
1 AA-AAGAA-AAGAAT
39446601 AAGAAGAAGAAGAAT
1 AA-AAGAA-AAGAAT
*
39446616 AAATAAAAAAGAA-
1 AAA-AGAAAAGAAT
39446629 AAAAGAAAAGAA
1 AAAAGAAAAGAA
39446641 AAAGGAGAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
12 8 0.17
13 5 0.11
14 11 0.24
15 22 0.48
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAGAAT
Found at i:39447655 original size:46 final size:46
Alignment explanation
Indices: 39447451--39447647 Score: 261
Period size: 46 Copynumber: 4.3 Consensus size: 46
39447441 ACCCAGATCA
* * * * *
39447451 ATGGATTAAAGAAGATACAAATCCTGTAACCC-TAAGTTACAGTGGG
1 ATGGATTGAAGAAGATACAAATCATAT-ACCCTTGAGTTGCAGTGGG
* *
39447497 ATGGATTGAAGAAGATACAAATCTTATACCCCTGAGTTGCAGTGGG
1 ATGGATTGAAGAAGATACAAATCATATACCCTTGAGTTGCAGTGGG
* *
39447543 ATGGATTGAAGAAGATACAAATCCTATACCCTTGAGTTGCCGTGGG
1 ATGGATTGAAGAAGATACAAATCATATACCCTTGAGTTGCAGTGGG
* *
39447589 ATGGATTGAAGATGATACAAATCATATACCCTTGAGTTGTAGTGGG
1 ATGGATTGAAGAAGATACAAATCATATACCCTTGAGTTGCAGTGGG
* *
39447635 GTGGATAGAAGAA
1 ATGGATTGAAGAA
39447648 ACCACAAAGT
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 4 0.03
46 131 0.97
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.26
Consensus pattern (46 bp):
ATGGATTGAAGAAGATACAAATCATATACCCTTGAGTTGCAGTGGG
Found at i:39448302 original size:143 final size:143
Alignment explanation
Indices: 39448044--39448405 Score: 496
Period size: 143 Copynumber: 2.5 Consensus size: 143
39448034 CATCATGGCA
**
39448044 AATCTTATCTCCCTAAAGTTGTGGTGGA-ATAGATTGAAGCCACAAGCCTTATCTTCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGA-AGATTGAAGCCACAAGCCTTATCTTCCTGAAGTT
* * *
39448108 GCAGCGGAGCAGACTAATGACAACGAATATTATTTCCCTGAACTTGCAGTGGAACAGATTAAAGC
65 GCAGCGGAGCAGACTAATGACAACGAACATCATTTCCCTGAACTTACAGTGGAACAGATTAAAGC
39448173 TAAAAATTATGGTG
130 TAAAAATTATGGTG
* * * * * *
39448187 AATCTTATCTCCTTGAAGTTGCAGTTGAGCAGATTGAAGCCACTAGCCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGCCACAAGCCTTATCTTCCTGAAGTTG
* * * * *
39448252 CAGCGGAGCAGACTGAA-GATAGCGGACCTCATTTCCCT-AACGTTATAGTGGAACAGATTAAAG
66 CAGCGGAGCAGACT-AATGACAACGAACATCATTTCCCTGAAC-TTACAGTGGAACAGATTAAAG
*
39448315 CTACAAATTATGGTG
129 CTAAAAATTATGGTG
*
39448330 AATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGCCACCAGCCTTATCTTCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGCCACAAGCCTTATCTTCCTGAAGTTG
* *
39448395 TAGCAGAGCAG
66 CAGCGGAGCAG
39448406 GTTGAAATTA
Statistics
Matches: 191, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
142 3 0.02
143 186 0.97
144 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (143 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGCCACAAGCCTTATCTTCCTGAAGTTG
CAGCGGAGCAGACTAATGACAACGAACATCATTTCCCTGAACTTACAGTGGAACAGATTAAAGCT
AAAAATTATGGTG
Found at i:39448435 original size:45 final size:44
Alignment explanation
Indices: 39448376--39448527 Score: 146
Period size: 45 Copynumber: 3.4 Consensus size: 44
39448366 AAGCCACCAG
* * *
39448376 CCTTATCT-TCCTGAAGTTGTAGCAGAGCAGGTTGAAATTACCGAT
1 CCTTATCTCT-CTGAAGTTGCAGTAGAGCAGGTTGAAA-TACCAAT
* * * * *
39448421 CCTTATCTCTCTGAACTTGCAGTAGAGTAGGATAAAATACACAAA
1 CCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATAC-CAAT
* * *
39448466 CCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAATACCAAT
1 CCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATACCAAT
*
39448510 TCTTATCTC-CTTGAAGTT
1 CCTTATCTCTC-TGAAGTT
39448528 CCAACAAAGT
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
43 1 0.01
44 21 0.24
45 64 0.74
46 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (44 bp):
CCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAATACCAAT
Found at i:39448797 original size:44 final size:44
Alignment explanation
Indices: 39448333--39448799 Score: 138
Period size: 44 Copynumber: 10.5 Consensus size: 44
39448323 TATGGTGAAT
* * * * * *
39448333 CTTATCTCCCTAAAGTTGCAGTGGAGAAGATTGAAGCCACCAGC
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCCACAATC
* ** ** * * *** *
39448377 CTTATCTTCCTGAAGTTGTAGCAGAGCAGGTTGAAATTACCGATC
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCCA-CAATC
* * * * * ** ** *
39448422 CTTATCTCTCTGAACTTGCAGTAGAGTAGGATAAAATACACAAAC
1 CTTATCTCCCTGAAGTTACAGTGGAGCA-GATCGAAGCCACAATC
* * ** *
39448467 CTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAA-ATACCAATT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCCA-CAATC
* * **** * * *
39448511 CTTATCTCCTTGAAGTTCCAACAAAGTAGATTGAAGCTACAAAT-
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCCAC-AATC
* * * *
39448555 CTCT-TCTCCTTGAAATTACATTGGAACAGATCGAAGCCACAATC
1 CT-TATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCCACAATC
* * * * * * ** **
39448599 TTTATCTCTCTGAAGCTACAATAGAGTAGGATAAAAATACACGAA-C
1 CTTATCTCCCTGAAGTTACAGTGGAGCA-GAT-CGAAGCCAC-AATC
** * *** *
39448645 CTTATCTCCCTGAAGTTGTAGTGGAGCA-AGTTGAAATTACCAATT
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGA-TCGAAGCCA-CAATC
* * * * *
39448690 CTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTACAAATC
1 CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCCAC-AATC
* * *
39448735 TCTT-T-TCCCAGAAATTACATTGGAGCAGATCGAAGCCACAATC
1 -CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCCACAATC
*
39448778 CTTATCTCTCTGAAGTTACAGT
1 CTTATCTCCCTGAAGTTACAGT
39448800 AAAGCAGGAT
Statistics
Matches: 300, Mismatches: 104, Indels: 38
0.68 0.24 0.09
Matches are distributed among these distances:
42 3 0.01
43 11 0.04
44 154 0.51
45 95 0.32
46 35 0.12
47 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGCCACAATC
Found at i:39448972 original size:179 final size:177
Alignment explanation
Indices: 39448422--39448978 Score: 751
Period size: 179 Copynumber: 3.1 Consensus size: 177
39448412 ATTACCGATC
* * *
39448422 CTTATCTCTCTGAACTTGCAGTAGAGTAGGAT-AAAATACACAAACCTTATCTCCCTGAAGTTAC
1 CTTATCTCTCTGAAGTTACAGTAGAGTAGGATAAAAATACACAAACCTTATCTCCCTGAAGTTGC
* * ** *
39448486 AGTGGAGCAGGTTGAAA-TACCAATTCTTATCTCCTTGAAGTTCCAACAAAGTAGATTGAAGCTA
66 AGTGGAGCAAGTTGAAATTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTA
*
39448550 CAAATCTCTTCTCCTTGAAATTACATTGGAACAGATCGAAGCCACAAT
131 CAAATCTCTTCTCC-TGAAATTACATTGGAGCAGATCGAAGCCACAAT
* * *
39448598 CTTTATCTCTCTGAAGCTACAATAGAGTAGGATAAAAATACACGAACCTTATCTCCCTGAAGTTG
1 C-TTATCTCTCTGAAGTTACAGTAGAGTAGGATAAAAATACACAAACCTTATCTCCCTGAAGTTG
*
39448663 TAGTGGAGCAAGTTGAAATTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCT
65 CAGTGGAGCAAGTTGAAATTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCT
* *
39448728 ACAAATCTCTTTTCCCAGAAATTACATTGGAGCAGATCGAAGCCACAAT
130 ACAAATCTCTTCT-CCTGAAATTACATTGGAGCAGATCGAAGCCACAAT
* * * * *
39448777 CCTTATCTCTCTGAAGTTACAGTAAAGCAGGATAAAAATACATAAACCTTTTCTCCTTGAAGTTG
1 -CTTATCTCTCTGAAGTTACAGTAGAGTAGGATAAAAATACACAAACCTTATCTCCCTGAAGTTG
* * * * *
39448842 CAGTGGAACAAGTTGAAATTATCAATTCTTATCTCCTTTAAGCTCCAGTGGAGTAGATCGAAGCT
65 CAGTGGAGCAAGTTGAAATTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCT
* * * * *
39448907 ACAAATCTCATCACTCTGAAATTACATTGGAGTAAATCGAAGCTACAAGT
130 ACAAATCTCTTCTC-CTGAAATTACATTGGAGCAGATCGAAGCCACAA-T
*
39448957 CTTATCT-TCCTGAAGTTGCAGT
1 CTTATCTCT-CTGAAGTTACAGT
39448979 GGGGCTACTT
Statistics
Matches: 336, Mismatches: 37, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
176 1 0.00
177 27 0.08
178 47 0.14
179 257 0.76
180 4 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (177 bp):
CTTATCTCTCTGAAGTTACAGTAGAGTAGGATAAAAATACACAAACCTTATCTCCCTGAAGTTGC
AGTGGAGCAAGTTGAAATTACCAATTCTTATCTCCTTGAAGTTCCAGCGGAGTAGATCGAAGCTA
CAAATCTCTTCTCCTGAAATTACATTGGAGCAGATCGAAGCCACAAT
Found at i:39449966 original size:17 final size:17
Alignment explanation
Indices: 39449944--39449985 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
39449934 CCATGACCAG
*
39449944 AGACCCGACCTGAGACC
1 AGACCCGACCCGAGACC
39449961 AGACCCGACCCGAGACC
1 AGACCCGACCCGAGACC
*
39449978 CGACCCGA
1 AGACCCGA
39449986 GTGTGACCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.45, G:0.24, T:0.02
Consensus pattern (17 bp):
AGACCCGACCCGAGACC
Found at i:39449976 original size:12 final size:12
Alignment explanation
Indices: 39449961--39449986 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39449951 ACCTGAGACC
39449961 AGACCCGACCCG
1 AGACCCGACCCG
39449973 AGACCCGACCCG
1 AGACCCGACCCG
39449985 AG
1 AG
39449987 TGTGACCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.46, G:0.27, T:0.00
Consensus pattern (12 bp):
AGACCCGACCCG
Found at i:39453305 original size:30 final size:30
Alignment explanation
Indices: 39453259--39453319 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
39453249 TTCCTGAGCC
39453259 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * *
39453289 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
39453319 T
1 T
39453320 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:39455906 original size:40 final size:40
Alignment explanation
Indices: 39455851--39455930 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
39455841 TTGAAATATG
*
39455851 AATGAAATTTTATGGCCCGTATTTTAGTTTAATGTTTGTA
1 AATGAAATTATATGGCCCGTATTTTAGTTTAATGTTTGTA
39455891 AATGAAATTATATGGCCCGTATTTTAGTTTAATGTTTGTA
1 AATGAAATTATATGGCCCGTATTTTAGTTTAATGTTTGTA
39455931 TGTTTGTCTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (40 bp):
AATGAAATTATATGGCCCGTATTTTAGTTTAATGTTTGTA
Found at i:39456158 original size:46 final size:46
Alignment explanation
Indices: 39456025--39456173 Score: 125
Period size: 46 Copynumber: 3.3 Consensus size: 46
39456015 ACTTGTGTGA
* * *
39456025 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGC-ATTGAGACG-AGT
1 GCTAGTGTAAGACATG-CTCGGACAT-GCATCGGCTA-CGAGATGTAGT
* * *
39456072 GCTAGTGTAAGACATGTTCGGGACATGCTTCTGCCT-CGAGATGTAAG-
1 GCTAGTGTAAGACATGCTC-GGACATGCATC-GGCTACGAGATGT-AGT
39456119 G-TAGTGTAAGACATGACTCGGACATGCATCGGCTACGAGATGT-GT
1 GCTAGTGTAAGACATG-CTCGGACATGCATCGGCTACGAGATGTAGT
39456164 -C-AGTGTAAGA
1 GCTAGTGTAAGA
39456174 TGATGTCTAG
Statistics
Matches: 84, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
44 10 0.12
45 3 0.04
46 42 0.50
47 27 0.32
48 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGCTCGGACATGCATCGGCTACGAGATGTAGT
Found at i:39461181 original size:7 final size:7
Alignment explanation
Indices: 39461169--39461200 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
39461159 GGAAGTGTTT
39461169 TTTTTTC
1 TTTTTTC
39461176 TTTTTTC
1 TTTTTTC
39461183 -TTTTTC
1 TTTTTTC
39461189 TTTTTTC
1 TTTTTTC
39461196 TTTTT
1 TTTTT
39461201 GAAAAAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:39461188 original size:13 final size:13
Alignment explanation
Indices: 39461166--39461200 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
39461156 GGAGGAAGTG
39461166 TTTT-TTTTTCTT
1 TTTTCTTTTTCTT
39461178 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
39461191 TTTTCTTTTT
1 TTTTCTTTTT
39461201 GAAAAAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:39461346 original size:15 final size:15
Alignment explanation
Indices: 39461314--39461342 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39461304 ATTTTTAGTG
39461314 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
39461329 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
39461343 ATTTTTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:39464159 original size:168 final size:168
Alignment explanation
Indices: 39463866--39464185 Score: 469
Period size: 168 Copynumber: 1.9 Consensus size: 168
39463856 GAAGTATATG
* * * *
39463866 TGGCATCGATATGTGATTCCAATATATGTGTGCGAGTAAGTCCACGTTTCGTACGTTGGCATCGA
1 TGGCATCGATATGTGACTCCAATATATGTGTGCGAGTAAGTCCACGTTTCATACATTGACATCGA
* * * *
39463931 TATGTGACTCTGATATATGTGTGCGAGTAAGTCCGCATTTAATACATTAGCATTGATATGTGATT
66 TATGTGACTCTGATATATGAGTGCGAGTAAGACCACATTTAATACATTAGCATCGATATGTGATT
* **
39463996 CTGATATATGTGTGCGAGTAAGTCCACATTTCATACGT
131 CCGATATATGTGTAAGAGTAAGTCCACATTTCATACGT
** *
39464034 TGGCATCGATATGTGACTCTGATATATGTGTGCGAGTAAGTCTACGTTTCATACATTGACATCGA
1 TGGCATCGATATGTGACTCCAATATATGTGTGCGAGTAAGTCCACGTTTCATACATTGACATCGA
* * * * *
39464099 TATGTGACTTTGATATATGAGTGTGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATT
66 TATGTGACTCTGATATATGAGTGCGAGTAAGACCACATTTAATACATTAGCATCGATATGTGATT
39464164 CCGATATATGTGTAAGAGTAAG
131 CCGATATATGTGTAAGAGTAAG
39464186 ACCCTGTATG
Statistics
Matches: 133, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
168 133 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (168 bp):
TGGCATCGATATGTGACTCCAATATATGTGTGCGAGTAAGTCCACGTTTCATACATTGACATCGA
TATGTGACTCTGATATATGAGTGCGAGTAAGACCACATTTAATACATTAGCATCGATATGTGATT
CCGATATATGTGTAAGAGTAAGTCCACATTTCATACGT
Found at i:39464188 original size:56 final size:56
Alignment explanation
Indices: 39463866--39464185 Score: 426
Period size: 56 Copynumber: 5.7 Consensus size: 56
39463856 GAAGTATATG
** *
39463866 TGGCATCGATATGTGATTCCAATATATGTGTGCGAGTAAGTCCACGTTTCGTACGT
1 TGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAGTCCACGTTTCATACGT
* * * * *
39463922 TGGCATCGATATGTGACTCTGATATATGTGTGCGAGTAAGTCCGCATTTAATACAT
1 TGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAGTCCACGTTTCATACGT
* * *
39463978 TAGCATTGATATGTGATTCTGATATATGTGTGCGAGTAAGTCCACATTTCATACGT
1 TGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAGTCCACGTTTCATACGT
* * *
39464034 TGGCATCGATATGTGACTCTGATATATGTGTGCGAGTAAGTCTACGTTTCATACAT
1 TGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAGTCCACGTTTCATACGT
* * * * *
39464090 TGACATCGATATGTGACTT-TGATATATGAGTGTGAGTAAGACCACGTTTAATACGT
1 TGGCATCGATATGTGA-TTCTGATATATGTGTGCGAGTAAGTCCACGTTTCATACGT
* **
39464146 TGGCATCGATATGTGATTCCGATATATGTGTAAGAGTAAG
1 TGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAG
39464186 ACCCTGTATG
Statistics
Matches: 229, Mismatches: 33, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
55 2 0.01
56 226 0.99
57 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (56 bp):
TGGCATCGATATGTGATTCTGATATATGTGTGCGAGTAAGTCCACGTTTCATACGT
Found at i:39465830 original size:29 final size:27
Alignment explanation
Indices: 39465812--39465881 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
39465802 ATATTAAGTC
39465812 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
39465839 CGCACACTTAGTTCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
39465867 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
39465882 GTACAATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:39465874 original size:28 final size:28
Alignment explanation
Indices: 39465812--39465909 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
39465802 ATATTAAGTC
*
39465812 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
39465839 CGCACACTTAGTTCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
39465867 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
39465896 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39465910 CAATCTCATG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 21 0.34
28 22 0.35
29 19 0.31
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:39471313 original size:40 final size:40
Alignment explanation
Indices: 39471252--39471473 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
39471242 TATTCGAATG
* *
39471252 ATATTCGGGCTAAGTCTCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
39471292 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
39471332 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
*
39471372 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
* *
39471412 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-TTGACT
*
39471452 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
39471474 TACTTGGGTT
Statistics
Matches: 171, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 14 0.08
40 154 0.90
41 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
Found at i:39473024 original size:43 final size:43
Alignment explanation
Indices: 39472975--39473130 Score: 124
Period size: 43 Copynumber: 3.7 Consensus size: 43
39472965 ATGTGTTCTT
*
39472975 ATGTAAGACCACGTCTGGGATGTTGGCATCGATATGTGATTAC
1 ATGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTAC
* * * * * *
39473018 ATGTAAGACCATGTCTGGGACATCGACATCG-TATTTAATT-C
1 ATGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTAC
* * * * *
39473059 GTGTAAGACC-CTATTTGTGATAG-TGGCATCGATATGTGA-TAGC
1 ATGTAAGACCAC-GTCTGGGA-CGTTGGCATCGATATGTGATTA-C
* *
39473102 ATGTAAGACCATGTCTGAGACGTTGGCAT
1 ATGTAAGACCACGTCTGGGACGTTGGCAT
39473131 TGTACGATAT
Statistics
Matches: 82, Mismatches: 24, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
41 22 0.27
42 13 0.16
43 47 0.57
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
ATGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTAC
Found at i:39479248 original size:12 final size:12
Alignment explanation
Indices: 39479231--39479255 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39479221 AGAGGAACAA
39479231 ATGGAAAAGATG
1 ATGGAAAAGATG
39479243 ATGGAAAAGATG
1 ATGGAAAAGATG
39479255 A
1 A
39479256 CTACAATGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
ATGGAAAAGATG
Found at i:39481714 original size:24 final size:24
Alignment explanation
Indices: 39481656--39481716 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
39481646 TTAGTCGTTT
*
39481656 TGAGCTTCCTATTATATGTTCTAG
1 TGAGCTTCCTGTTATATGTTCTAG
*
39481680 CGAGCTTCCTGTTATATGGTT-TAG
1 TGAGCTTCCTGTTATAT-GTTCTAG
39481704 TGAGCTTCCTGTT
1 TGAGCTTCCTGTT
39481717 TTAGCTCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.44
Consensus pattern (24 bp):
TGAGCTTCCTGTTATATGTTCTAG
Found at i:39481844 original size:27 final size:26
Alignment explanation
Indices: 39481776--39481845 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
39481766 ACACACCTTA
*
39481776 GCTC-TTATGAGCATCCCAATTAAAG
1 GCTCTTTATGAGCTTCCCAATTAAAG
* **
39481801 GCTCTTCATGATATTCCC-ATTAAATTG
1 GCTCTTTATGAGCTTCCCAATTAAA--G
39481828 GCTCTTTATGAGCTTCCC
1 GCTCTTTATGAGCTTCCC
39481846 GATAATACTC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
25 10 0.29
26 9 0.26
27 16 0.46
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (26 bp):
GCTCTTTATGAGCTTCCCAATTAAAG
Found at i:39491696 original size:21 final size:21
Alignment explanation
Indices: 39491672--39491713 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
39491662 TTTGCCTAGG
*
39491672 ATATGAATTGAATTAAATTGA
1 ATATGAAATGAATTAAATTGA
*
39491693 ATATGAAATGGATTAAATTGA
1 ATATGAAATGAATTAAATTGA
39491714 TGTTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.36
Consensus pattern (21 bp):
ATATGAAATGAATTAAATTGA
Found at i:39498203 original size:41 final size:41
Alignment explanation
Indices: 39498174--39498517 Score: 483
Period size: 41 Copynumber: 8.4 Consensus size: 41
39498164 CATTTTTTAC
* *
39498174 TAAAACGCAGCTAAAAACC-GATCATTAGCGGCGCTTTAGG
1 TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
*
39498214 TAAAACGCCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
1 TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
39498255 TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
1 TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
*
39498296 TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTGGG
1 TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
* * * * *
39498337 TAAAACGCCGCTAAAAACTAGAGCATTAGCGGCGCCTTCGG
1 TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
* * * *
39498378 TAAAACACTGCTAAAAACCAGAGCATTAGCAGCGCTTTCGG
1 TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
* * ** *
39498419 TAAAACGCCGCTAAAAACCAGAGCATTAGCGGCATTTTCGG
1 TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
* *
39498460 TAAAACACCGCTAAAAACCCAGAGCATTAGCGGCGCTTTTGG
1 TAAAACACCGCTAAAAA-CCAGATCATTAGCGGCGCTTTAGG
*
39498502 TAAAACACTGCTAAAA
1 TAAAACACCGCTAAAA
39498518 GTCATAGAAC
Statistics
Matches: 279, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
40 18 0.06
41 225 0.81
42 36 0.13
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.19
Consensus pattern (41 bp):
TAAAACACCGCTAAAAACCAGATCATTAGCGGCGCTTTAGG
Found at i:39499393 original size:24 final size:23
Alignment explanation
Indices: 39499334--39499395 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
39499324 AGATAAATGT
*
39499334 ATATATATAAGATAAATATATATA
1 ATATATATATGA-AAATATATATA
* *
39499358 TTAT-TATTTGAAAATATATATAA
1 ATATATATATGAAAATATATAT-A
39499381 ATATATATATGAAAA
1 ATATATATATGAAAA
39499396 GTGGTTTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 10 0.32
23 9 0.29
24 12 0.39
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
ATATATATATGAAAATATATATA
Found at i:39507600 original size:20 final size:20
Alignment explanation
Indices: 39507575--39507623 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
39507565 GTTGTCTTAT
39507575 TTTTTAACAAATTAAACATG
1 TTTTTAACAAATTAAACATG
39507595 TTTTTAACAAATTAAACATG
1 TTTTTAACAAATTAAACATG
39507615 TTTTTAACA
1 TTTTTAACA
39507624 TAGTGAGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (20 bp):
TTTTTAACAAATTAAACATG
Found at i:39508061 original size:526 final size:526
Alignment explanation
Indices: 39507069--39508102 Score: 2014
Period size: 526 Copynumber: 2.0 Consensus size: 526
39507059 ATTTGTTTAT
*
39507069 TTTTTAACAAATTAAACATGTTTTTAACATAGTGAGTACAAACAAGTCTTAAGATTTGTTCACGC
1 TTTTTAACAAATTAAACATGTTTTTAACATAGTGAGTACAAACAAGTCTTAAGATCTGTTCACGC
* *
39507134 TCATGAAGATTACAACATCGCGAGATTAATAGGTTATTTGCAGAATCTTTTCATGAATGGTTAAG
66 TCACGAAGATTACAACATCGCGAGATTAATAGGTTATTCGCAGAATCTTTTCATGAATGGTTAAG
39507199 CCAAACGGTATGCAACTCAATATTTTATTGACAAATAATAATGTTTTCTCATAACATTTACAATT
131 CCAAACGGTATGCAACTCAATATTTTATTGACAAATAATAATGTTTTCTCATAACATTTACAATT
39507264 ACTCAATTTACTTTTGATTCAATAGGTTTGGAGTGGGAATATCGTTAATGACGAAGTTAAATGGC
196 ACTCAATTTACTTTTGATTCAATAGGTTTGGAGTGGGAATATCGTTAATGACGAAGTTAAATGGC
39507329 TTTCCCAAGGTCCGAATCGAGTAGTAAAAAGATATAGTGGCTTCATCATGAATGGATTCAGATTT
261 TTTCCCAAGGTCCGAATCGAGTAGTAAAAAGATATAGTGGCTTCATCATGAATGGATTCAGATTT
39507394 CATACCAAATATCGCGAGAGATTGAGGAGAACTCAAAATTGTGGAGTAGTTGTTAATTCTTTAAT
326 CATACCAAATATCGCGAGAGATTGAGGAGAACTCAAAATTGTGGAGTAGTTGTTAATTCTTTAAT
39507459 TACAAGTTATGCTAGTGCTAGGGACAGTAATCCTGTGGAGGGAAATGTGGAGTATTACGGACTTC
391 TACAAGTTATGCTAGTGCTAGGGACAGTAATCCTGTGGAGGGAAATGTGGAGTATTACGGACTTC
*
39507524 TAACCGACATTATTGAGTTGGATTACTATGGAAATTGGAAAGTTGTCTTATTTTTTAACAAATTA
456 TAACCGACATTATTGAGTTGGATTACTATGGAAAATGGAAAGTTGTCTTATTTTTTAACAAATTA
39507589 AACATG
521 AACATG
39507595 TTTTTAACAAATTAAACATGTTTTTAACATAGTGAGTACAAACAAGTCTTAAGATCTGTTCACGC
1 TTTTTAACAAATTAAACATGTTTTTAACATAGTGAGTACAAACAAGTCTTAAGATCTGTTCACGC
*
39507660 TTACGAAGATTACAACATCGCGAGATTAATAGGTTATTCGCAGAATCTTTTCATGAATGGTTAAG
66 TCACGAAGATTACAACATCGCGAGATTAATAGGTTATTCGCAGAATCTTTTCATGAATGGTTAAG
39507725 CCAAACGGTATGCAACTCAATATTTTATTGACAAATAATAATGTTTTCTCATAACATTTACAATT
131 CCAAACGGTATGCAACTCAATATTTTATTGACAAATAATAATGTTTTCTCATAACATTTACAATT
39507790 ACTCAATTTACTTTTGATTCAATAGGTTTGGAGTGGGAATATCGTTAATGACGAAGTTAAATGGC
196 ACTCAATTTACTTTTGATTCAATAGGTTTGGAGTGGGAATATCGTTAATGACGAAGTTAAATGGC
*
39507855 TTTTCCAAGGTCCGAATCGAGTAGTAAAAAGATATAGTGGCTTCATCATGAATGGATTCAGATTT
261 TTTCCCAAGGTCCGAATCGAGTAGTAAAAAGATATAGTGGCTTCATCATGAATGGATTCAGATTT
39507920 CATACCAAATATCGCGAGAGATTGAGGAGAACTCAAAATTGTGGAGTAGTTGTTAATTCTTTAAT
326 CATACCAAATATCGCGAGAGATTGAGGAGAACTCAAAATTGTGGAGTAGTTGTTAATTCTTTAAT
39507985 TACAAGTTATGCTAGTGCTAGGGACAGTAATCCTGTGGAGGGAAATGTGGAGTATTACGGACTTC
391 TACAAGTTATGCTAGTGCTAGGGACAGTAATCCTGTGGAGGGAAATGTGGAGTATTACGGACTTC
39508050 TAACCGACATTATTGAGTTGGATTACTATGGAAAATGGAAAGTTGTCTTATTT
456 TAACCGACATTATTGAGTTGGATTACTATGGAAAATGGAAAGTTGTCTTATTT
39508103 CGATGCGATT
Statistics
Matches: 502, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
526 502 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (526 bp):
TTTTTAACAAATTAAACATGTTTTTAACATAGTGAGTACAAACAAGTCTTAAGATCTGTTCACGC
TCACGAAGATTACAACATCGCGAGATTAATAGGTTATTCGCAGAATCTTTTCATGAATGGTTAAG
CCAAACGGTATGCAACTCAATATTTTATTGACAAATAATAATGTTTTCTCATAACATTTACAATT
ACTCAATTTACTTTTGATTCAATAGGTTTGGAGTGGGAATATCGTTAATGACGAAGTTAAATGGC
TTTCCCAAGGTCCGAATCGAGTAGTAAAAAGATATAGTGGCTTCATCATGAATGGATTCAGATTT
CATACCAAATATCGCGAGAGATTGAGGAGAACTCAAAATTGTGGAGTAGTTGTTAATTCTTTAAT
TACAAGTTATGCTAGTGCTAGGGACAGTAATCCTGTGGAGGGAAATGTGGAGTATTACGGACTTC
TAACCGACATTATTGAGTTGGATTACTATGGAAAATGGAAAGTTGTCTTATTTTTTAACAAATTA
AACATG
Found at i:39509219 original size:14 final size:15
Alignment explanation
Indices: 39509200--39509232 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39509190 GAGAGACAAT
39509200 AAAAGAAT-TTTGAA
1 AAAAGAATATTTGAA
*
39509214 AAAAGAATATTTTAA
1 AAAAGAATATTTGAA
39509229 AAAA
1 AAAA
39509233 CCCATAAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (15 bp):
AAAAGAATATTTGAA
Found at i:39514955 original size:20 final size:20
Alignment explanation
Indices: 39514930--39514971 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
39514920 AGAAAGAGAA
39514930 TGAAGTAAATATCGCGAGTG
1 TGAAGTAAATATCGCGAGTG
39514950 TGAAGTAAATATCGCGAGTG
1 TGAAGTAAATATCGCGAGTG
39514970 TG
1 TG
39514972 TACAATAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.26
Consensus pattern (20 bp):
TGAAGTAAATATCGCGAGTG
Found at i:39520390 original size:25 final size:25
Alignment explanation
Indices: 39520354--39520401 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
39520344 CACAAACGCA
39520354 GCTCTTTATGAGCGTCCTAATATAG
1 GCTCTTTATGAGCGTCCTAATATAG
* *
39520379 GCTCTTTTTGAGCTTCCTAATAT
1 GCTCTTTATGAGCGTCCTAATAT
39520402 GACTTGCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (25 bp):
GCTCTTTATGAGCGTCCTAATATAG
Found at i:39521952 original size:30 final size:30
Alignment explanation
Indices: 39521918--39521976 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
39521908 TGAAATTTTG
39521918 TGAAAAATTCTTTTAGTTTC-GATTTACTCC
1 TGAAAAATTCTTTTAG-TTCAGATTTACTCC
39521948 TGAAAAATTCTTTTAGTTCAGATTTACTC
1 TGAAAAATTCTTTTAGTTCAGATTTACTC
39521977 TTGACTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (30 bp):
TGAAAAATTCTTTTAGTTCAGATTTACTCC
Found at i:39524918 original size:50 final size:49
Alignment explanation
Indices: 39524862--39525107 Score: 191
Period size: 50 Copynumber: 5.2 Consensus size: 49
39524852 TGGGTTAGAT
39524862 TGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGAAGCAAGA
1 TGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGTG-AGCAAGA
* * * * *
39524912 TGAAGCTAC---A---AATCCTATAC-CCTTGAAGTGGCAGTGGGTC-GGA
1 TGAAGCTACAATAGCGAATCTTAT-CTCCCTGAAGTTGCAGTGAG-CAAGA
*
39524955 TTGTAGCTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGA
1 -TGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGT-GAGCAAGA
* * * * *
39525006 TAAAGCTAC---A---AATCCTATAC-CCTTGAAGTTGCAGTGGGTC-GGA
1 TGAAGCTACAATAGCGAATCTTAT-CTCCCTGAAGTTGCAGTGAG-CAAGA
*
39525049 TTGTAGCTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGCAGCAAGA
1 -TGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGTG-AGCAAGA
39525100 TGAAGCTA
1 TGAAGCTA
39525108 GAAATCTTGT
Statistics
Matches: 148, Mismatches: 24, Indels: 48
0.67 0.11 0.22
Matches are distributed among these distances:
43 7 0.05
44 59 0.40
45 2 0.01
47 4 0.03
49 2 0.01
50 67 0.45
51 7 0.05
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (49 bp):
TGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGAGCAAGA
Found at i:39524940 original size:44 final size:43
Alignment explanation
Indices: 39524891--39525041 Score: 126
Period size: 44 Copynumber: 3.3 Consensus size: 43
39524881 CTTATCTCCC
39524891 TGAAGTTGCAGTGAAGCAAGATGAAGCTACAAATCCTATACCCT
1 TGAAGTTGCAGTG-AGCAAGATGAAGCTACAAATCCTATACCCT
* * * * * *
39524935 TGAAGTGGCAGTGGGTC-GGATTGTAGCTACAATAGCGAATCT-TATCTCCC
1 TGAAGTTGCAGTGAG-CAAGA-TGAAGCTACAA-ATC----CTATA-C-CCT
*
39524985 TGAAGTTGCAGTGGAGCAAGATAAAGCTACAAATCCTATACCCT
1 TGAAGTTGCAGT-GAGCAAGATGAAGCTACAAATCCTATACCCT
39525029 TGAAGTTGCAGTG
1 TGAAGTTGCAGTG
39525042 GGTCGGATTG
Statistics
Matches: 82, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
43 4 0.05
44 37 0.45
45 5 0.06
46 2 0.02
48 2 0.02
49 5 0.06
50 23 0.28
51 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
TGAAGTTGCAGTGAGCAAGATGAAGCTACAAATCCTATACCCT
Found at i:39524988 original size:94 final size:94
Alignment explanation
Indices: 39524827--39525746 Score: 929
Period size: 94 Copynumber: 9.8 Consensus size: 94
39524817 GTGAAACCAT
* * * **
39524827 AAATCCTATACCCCTAAAGTTGCAATGGGTTAGATTGAAGCTACAATAGCGAATCTTATCTCCCT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCCT
*
39524892 GAAGTTGCAGTGAAGCAAGATGAAGCTAC
66 GAAGTTGCAGTGGAGCAAGATGAAGCTAC
* *
39524921 AAATCCTATACCCTTGAAGTGGCAGTGGGTCGGATTGTAGCTACAATAGCGAATCTTATCTCCCT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCCT
*
39524986 GAAGTTGCAGTGGAGCAAGATAAAGCTAC
66 GAAGTTGCAGTGGAGCAAGATGAAGCTAC
*
39525015 AAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGTAGCTACAATAGCGAATCTTATCTCCCT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCCT
* *
39525080 GAAGTTGCAGTGCAGCAAGATGAAGCTAG
66 GAAGTTGCAGTGGAGCAAGATGAAGCTAC
* * * * * * * *** *
39525109 AAATCTTGTA-ACTCTGAAGTTGTAGTGGTTTGGAATGAAGCTACAATAAAAAATCTTATTTCCC
1 AAATCCTATACCCT-TGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCC
*
39525173 TGAAGTTGTTA-TGGAGCAAGATGAAGCTAC
65 TGAAGTTG-CAGTGGAGCAAGATGAAGCTAC
* * * * **
39525203 AAATCCTATACCCTTGAAGTTGCAATGGGTCGGATTGAAGCTACCATAGCAAATCTTATCGCTTT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCCT
* * * *
39525268 AAAGTTGCAGTGGAGTAAAATGAAGTTAC
66 GAAGTTGCAGTGGAGCAAGATGAAGCTAC
* * * * *
39525297 AAATCTTATACCCCTAAAGTTGCAGTGGGTCAGATTGAAGCTACTATAGCGAATCTTATCTCCCT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCCT
* * * *
39525362 AAAGTTGTAGTAGAGCAAGATGAAACTAC
66 GAAGTTGCAGTGGAGCAAGATGAAGCTAC
* * * * *
39525391 AAATCCTATA-CCTCTAAAGTTGTAGTGGGTCGAATTGAAGCTACCATAGAGAATCTTATCT-CC
1 AAATCCTATACCCT-TGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCC
* * *
39525454 TTAATGTTGTAGTGGAGCAAGATGAAGTTAC
65 TGAA-GTTGCAGTGGAGCAAGATGAAGCTAC
* * * * * * * *
39525485 AATTCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAACCACCATAAC-ATATCTTATCTCCC
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGA-ATCTTATCTCCC
* * * * * *
39525549 TAAAGCTGCAATGGGGCAAAATAAAGCTAC
65 TGAAGTTGCAGTGGAGCAAGATGAAGCTAC
* * * * * * * *
39525579 AAATCCAATACCCTTAAAGTTGCAGTGGGTCTGATTGAAGCTACCATAACAAATCTTTTCTCCTT
1 AAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCCT
** * *
39525644 GAAGTTGCAACGGAGTAAGGT-AGAGCTAC
66 GAAGTTGCAGTGGAGCAAGATGA-AGCTAC
* * * ** * * *
39525673 AAATCCTATATCCC-TAAAATTGCAATGAAAT-GGATTGAAACTACAATAACAAATCTTATCTCC
1 AAATCCTATA-CCCTTGAAGTTGCAGTG-GGTCGGATTGAAGCTACAATAGCGAATCTTATCTCC
* *
39525736 TTAAAGTTGCA
64 CTGAAGTTGCA
39525747 ATGAAACAAT
Statistics
Matches: 694, Mismatches: 119, Indels: 26
0.83 0.14 0.03
Matches are distributed among these distances:
93 12 0.02
94 667 0.96
95 15 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (94 bp):
AAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGAAGCTACAATAGCGAATCTTATCTCCCT
GAAGTTGCAGTGGAGCAAGATGAAGCTAC
Found at i:39525057 original size:44 final size:44
Alignment explanation
Indices: 39524915--39525060 Score: 136
Period size: 44 Copynumber: 3.2 Consensus size: 44
39524905 AGCAAGATGA
*
39524915 AGCTACAAATCCTATACCCTTGAAGTGGCAGTGGGTCGGATTGT
1 AGCTACAAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGT
* * * **
39524959 AGCTACAATAGCGAATCT-TATCTCCCTGAAGTTGCAGTGGAG-CAAGA-TAA
1 AGCTACAA-ATC----CTATA-C-CCTTGAAGTTGCAGTGG-GTC-GGATTGT
39525009 AGCTACAAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGT
1 AGCTACAAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGT
39525053 AGCTACAA
1 AGCTACAA
39525061 TAGCGAATCT
Statistics
Matches: 79, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
43 3 0.04
44 34 0.43
45 5 0.06
46 2 0.03
48 2 0.03
49 5 0.06
50 25 0.32
51 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (44 bp):
AGCTACAAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTGT
Found at i:39525292 original size:50 final size:48
Alignment explanation
Indices: 39525219--39525635 Score: 142
Period size: 44 Copynumber: 8.8 Consensus size: 48
39525209 TATACCCTTG
* ** * **
39525219 AAGTTGCAATGGGTCGGATTGAAGCTACCATAGCAAATCTTATCGCTTTA
1 AAGTTGCAGTGGGTCAAAATGAAGCTA-CATAGCAAATCTTATC-CCCTA
39525269 AAGTTGCAGTGGAGT-AAAATGAAG-T---TA-CAAATCTTATACCCCTA
1 AAGTTGCAGTGG-GTCAAAATGAAGCTACATAGCAAATCTTAT-CCCCTA
* * *
39525313 AAGTTGCAGTGGGTCAGATTGAAGCTACTATAGCGAATCTTATCTCCCTA
1 AAGTTGCAGTGGGTCAAAATGAAGCTAC-ATAGCAAATCTTATC-CCCTA
* * * * *
39525363 AAGTTGTAGTAGAG-CAAGATGAA---AC-TA-CAAATCCTATACCTCTA
1 AAGTTGCAGT-GGGTCAAAATGAAGCTACATAGCAAATCTTAT-CCCCTA
* * * *
39525407 AAGTTGTAGTGGGTCGAATTGAAGCTACCATAG-AGAATCTTATCTCCTTA
1 AAGTTGCAGTGGGTCAAAATGAAGCTA-CATAGCA-AATCTTATC-CCCTA
* * * * * *
39525457 ATGTTGTAGTGGAG-CAAGATGAAG-T---TA-CAATTCCTATACCCCTG
1 AAGTTGCAGTGG-GTCAAAATGAAGCTACATAGCAAATCTTAT-CCCCTA
* * * * * * *
39525501 AAGTTGTAGTGGGTCAGATTGAAACCACCATAACATATCTTATCTCCCTA
1 AAGTTGCAGTGGGTCAAAATGAAGCTA-CATAGCAAATCTTATC-CCCTA
* * * * * * * *
39525551 AAGCTGCAATGGGGCAAAATAAAGCTACAAATCCAA---TA-CCCTTA
1 AAGTTGCAGTGGGTCAAAATGAAGCTACATAGCAAATCTTATCCCCTA
** * *
39525595 AAGTTGCAGTGGGTCTGATTGAAGCTACCATAACAAATCTT
1 AAGTTGCAGTGGGTCAAAATGAAGCTA-CATAGCAAATCTT
39525636 TTCTCCTTGA
Statistics
Matches: 265, Mismatches: 66, Indels: 74
0.65 0.16 0.18
Matches are distributed among these distances:
43 5 0.02
44 110 0.42
45 18 0.07
46 2 0.01
47 3 0.01
48 2 0.01
49 17 0.06
50 103 0.39
51 5 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (48 bp):
AAGTTGCAGTGGGTCAAAATGAAGCTACATAGCAAATCTTATCCCCTA
Found at i:39525730 original size:282 final size:280
Alignment explanation
Indices: 39524827--39525744 Score: 1034
Period size: 282 Copynumber: 3.3 Consensus size: 280
39524817 GTGAAACCAT
* * *
39524827 AAATCCTATACCCCTAAAGTTGCAATGGGTTAGATTGAAGCTACAATAGCGAATCTTATCTCCCT
1 AAATCCTATA-CCCTAAAGTTGCAATGGGTTGGATTGAAGCTACAATAACAAATCTTATCTCCCT
* * *
39524892 GAAGTTGCAGTGAAGCAAGATGAAGCTACAAATCCTATACCCTTGAAGTGGCAGTGGGTCGGATT
65 GAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATT
* * * *
39524957 GTAGCTACAATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATAAAGCTACAAATCCT
130 GAAGCTACCATAGC-AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAAATAAAGCTACAAATCCT
* * *
39525022 ATACCCTTGAAGTTGCAGTGGGTCGGATTGTAGCTACAATAGCGAATCTTATCTCCCTGAAGTTG
194 ATACCCTTAAAGTTGCAGTGGGTCAGATTGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTG
* *
39525087 CAGTGCAGCAAGATGAAGCTAG
259 CAGTGGAGCAAGATGAAGCTAC
* * * * * * * * * *
39525109 AAATCTTGTAACTCTGAAGTTGTAGTGGTTTGGAATGAAGCTACAATAAAAAATCTTATTTCCCT
1 AAATCCTAT-ACCCTAAAGTTGCAATGGGTTGGATTGAAGCTACAATAACAAATCTTATCTCCCT
*
39525174 GAAGTTGTTA-TGGAGCAAGATGAAGCTACAAATCCTATACCCTTGAAGTTGCAATGGGTCGGAT
65 GAAGTTG-TAGTGGAGCAAGATGAAGCTACAAATCCTATACCCTTGAAGTTGCAGTGGGTCGGAT
* ** * * * *
39525238 TGAAGCTACCATAGCAAATCTTATCGCTTTAAAGTTGCAGTGGAGTAAAATGAAGTTACAAATCT
129 TGAAGCTACCATAGC-AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAAATAAAGCTACAAATCC
* * *
39525303 TATACCCCTAAAGTTGCAGTGGGTCAGATTGAAGCTACTATAGCGAATCTTATCTCCCTAAAGTT
193 TATACCCTTAAAGTTGCAGTGGGTCAGATTGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTT
* * *
39525368 GTAGTAGAGCAAGATGAAACTAC
258 GCAGTGGAGCAAGATGAAGCTAC
* * * * * *
39525391 AAATCCTATACCTCTAAAGTTGTAGTGGGTCGAATTGAAGCTACCATAGA-GAATCTTATCT-CC
1 AAATCCTATACC-CTAAAGTTGCAATGGGTTGGATTGAAGCTACAATA-ACAAATCTTATCTCCC
* * * * * *
39525454 TTAATGTTGTAGTGGAGCAAGATGAAGTTACAATTCCTATACCCCTGAAGTTGTAGTGGGTCAGA
64 TGAA-GTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCTTGAAGTTGCAGTGGGTCGGA
* * * * * *
39525519 TTGAAACCACCATAACATATCTTATCTCCCTAAAGCTGCAATGGGGCAAAATAAAGCTACAAATC
128 TTGAAGCTACCATAGCA-ATCTTATCTCCCTAAAGTTGCAGTGGAGCAAAATAAAGCTACAAATC
* * * * * * *
39525584 CAATACCCTTAAAGTTGCAGTGGGTCTGATTGAAGCTACCATAACAAATCTTTTCTCCTTGAAGT
192 CTATACCCTTAAAGTTGCAGTGGGTCAGATTGAAGCTACAATAGCGAATCTTATCTCCCTGAAGT
** * *
39525649 TGCAACGGAGTAAGGT-AGAGCTAC
257 TGCAGTGGAGCAAGATGA-AGCTAC
* *** * *
39525673 AAATCCTATATCCCTAAAATTGCAATGAAATGGATTGAAACTACAATAACAAATCTTATCTCCTT
1 AAATCCTATA-CCCTAAAGTTGCAATGGGTTGGATTGAAGCTACAATAACAAATCTTATCTCCCT
*
39525738 AAAGTTG
65 GAAGTTG
39525745 CAATGAAACA
Statistics
Matches: 525, Mismatches: 100, Indels: 22
0.81 0.15 0.03
Matches are distributed among these distances:
281 12 0.02
282 504 0.96
283 9 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (280 bp):
AAATCCTATACCCTAAAGTTGCAATGGGTTGGATTGAAGCTACAATAACAAATCTTATCTCCCTG
AAGTTGTAGTGGAGCAAGATGAAGCTACAAATCCTATACCCTTGAAGTTGCAGTGGGTCGGATTG
AAGCTACCATAGCAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAAATAAAGCTACAAATCCTAT
ACCCTTAAAGTTGCAGTGGGTCAGATTGAAGCTACAATAGCGAATCTTATCTCCCTGAAGTTGCA
GTGGAGCAAGATGAAGCTAC
Found at i:39534425 original size:32 final size:33
Alignment explanation
Indices: 39534383--39534450 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
39534373 TAAAATCGGT
*
39534383 AAATAGTATTTTCCAAAA-AAAAATATTTTTAG
1 AAATAATATTTTCCAAAATAAAAATATTTTTAG
*
39534415 AAATAATATTTTCCAAAATAAGAATATTTTTAG
1 AAATAATATTTTCCAAAATAAAAATATTTTTAG
39534448 AAA
1 AAA
39534451 AATTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (33 bp):
AAATAATATTTTCCAAAATAAAAATATTTTTAG
Found at i:39536071 original size:29 final size:29
Alignment explanation
Indices: 39536029--39536084 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
39536019 TGCCATATGG
39536029 CTCACCATTGTATGTATGATTTGTGAGTA
1 CTCACCATTGTATGTATGATTTGTGAGTA
* *
39536058 CTCACCATTGTATGTGTTATTTGTGAG
1 CTCACCATTGTATGTATGATTTGTGAG
39536085 CATATGGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (29 bp):
CTCACCATTGTATGTATGATTTGTGAGTA
Found at i:39537801 original size:8 final size:8
Alignment explanation
Indices: 39537790--39537815 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39537780 TTAAAAATTC
39537790 AAAATAAT
1 AAAATAAT
39537798 AAAATAAT
1 AAAATAAT
39537806 AAAATAAT
1 AAAATAAT
39537814 AA
1 AA
39537816 GAGCTGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:39540004 original size:100 final size:100
Alignment explanation
Indices: 39539826--39540006 Score: 238
Period size: 100 Copynumber: 1.8 Consensus size: 100
39539816 GTCACAAGTA
* *
39539826 AATAAATCCATAAATGGATCTAAGATTTATTCTACCTAGGTCCTGTCCAATGTACTGTCAATCCA
1 AATAAATCCATAAACGGATCTAAGATTTATTCTACCTAGGTCCTGTCCAATGCACTGTCAATCCA
*
39539891 GTCAGTCACATCTATGACTCTATCTTTTAAGAGTC
66 GTCAATCACATCTATGACTCTATCTTTTAAGAGTC
* * * * * * * *
39539926 AATAAATCTATAAACGGATCTAGGATTTATTCTA-CTTGGTTCCTGTTCGATGCACTGTTAGTCT
1 AATAAATCCATAAACGGATCTAAGATTTATTCTACCTAGG-TCCTGTCCAATGCACTGTCAATCC
*
39539990 AGTCAATCATATCTATG
65 AGTCAATCACATCTATG
39540007 TCTTTACCTT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
99 4 0.06
100 64 0.94
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (100 bp):
AATAAATCCATAAACGGATCTAAGATTTATTCTACCTAGGTCCTGTCCAATGCACTGTCAATCCA
GTCAATCACATCTATGACTCTATCTTTTAAGAGTC
Found at i:39546169 original size:10 final size:10
Alignment explanation
Indices: 39546154--39546190 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
39546144 AATTATTAAC
39546154 ATAATTAATT
1 ATAATTAATT
39546164 ATAATTAATT
1 ATAATTAATT
39546174 ATAATTAATT
1 ATAATTAATT
*
39546184 TTAATTA
1 ATAATTA
39546191 TTTTCAACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
ATAATTAATT
Found at i:39551851 original size:20 final size:20
Alignment explanation
Indices: 39551822--39551868 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
39551812 ATTTTGATAA
*
39551822 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
39551842 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
39551862 ACATGAT
1 ACATGAT
39551869 GTATTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:39551976 original size:24 final size:24
Alignment explanation
Indices: 39551917--39552023 Score: 180
Period size: 24 Copynumber: 4.4 Consensus size: 24
39551907 GGAGGAAGTG
39551917 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
39551941 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
39551966 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
39551990 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
39552013 TAAAAGAGGCT
1 TAAAAG-GGCT
39552024 AGCCCTCCAG
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
23 18 0.23
24 38 0.48
25 23 0.29
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:39551989 original size:49 final size:47
Alignment explanation
Indices: 39551917--39552023 Score: 178
Period size: 49 Copynumber: 2.2 Consensus size: 47
39551907 GGAGGAAGTG
39551917 TAAAAGGGCTTATGCCCCAGTTATGATAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTATGA-AAAGGGCTT-TGCCCCAGTTAT
*
39551966 TAAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTATGAAAAGGGCTTTGCCCCAGTTAT
39552013 TAAAAGAGGCT
1 TAAAAG-GGCT
39552024 AGCCCTCCAG
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
47 18 0.32
48 13 0.23
49 25 0.45
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (47 bp):
TAAAAGGGCTTATGCCCCAGTTATGAAAAGGGCTTTGCCCCAGTTAT
Found at i:39552266 original size:31 final size:31
Alignment explanation
Indices: 39552231--39552293 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
39552221 CGTTTACAGT
*
39552231 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATACGAAATATGA
* **
39552262 AAAGGCTTCGGCCTAGTGTTACGAAATATGA
1 AAAGGCTTCGGCCCAGTAATACGAAATATGA
39552293 A
1 A
39552294 GTGTGAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATACGAAATATGA
Found at i:39553954 original size:49 final size:51
Alignment explanation
Indices: 39553881--39554009 Score: 156
Period size: 49 Copynumber: 2.6 Consensus size: 51
39553871 TTGTGAGGTC
* **
39553881 ACATGTGTAGTACTAAATGCAGGCTACTACGTGTAC-CGGATAA-TT-GGTT
1 ACATGTGTAGTACTAAGTGCAGGCTACTACACGTACTC-GATAACTTCGGTT
* ** *
39553930 GCATGTGTAGTACTCGGTGCAGGCTACTATACGTACTCGATAACTTCGGTT
1 ACATGTGTAGTACTAAGTGCAGGCTACTACACGTACTCGATAACTTCGGTT
*
39553981 ACGTGTGTAGTACTAAGTGCAGGCTACTA
1 ACATGTGTAGTACTAAGTGCAGGCTACTA
39554010 TGCGTACCAG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 34 0.52
50 3 0.05
51 29 0.44
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (51 bp):
ACATGTGTAGTACTAAGTGCAGGCTACTACACGTACTCGATAACTTCGGTT
Found at i:39559076 original size:49 final size:49
Alignment explanation
Indices: 39558997--39559178 Score: 256
Period size: 49 Copynumber: 3.7 Consensus size: 49
39558987 TCTATTGTGA
39558997 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
* * * * **
39559046 GGTCGCATGTGTAGTACTAAGTGCATGCTACTATGCGTACCCGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAA-TT
*
39559096 CGATCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
* * *
39559146 GGTCGCATGTGTAGTACCAAGTGCAGGATACTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTA
39559179 TGCGTACCAG
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 70 0.61
50 4 0.04
51 40 0.35
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
Found at i:39559178 original size:100 final size:100
Alignment explanation
Indices: 39558999--39559191 Score: 350
Period size: 100 Copynumber: 1.9 Consensus size: 100
39558989 TATTGTGAGG
*
39558999 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTACC
* * *
39559064 AAGTGCATGCTACTATGCGTACCCGATAACTTCGA
66 AAGTGCAGGATACTATGCGTACCAGATAACTTCGA
39559099 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTACC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTACC
39559164 AAGTGCAGGATACTATGCGTACCAGATA
66 AAGTGCAGGATACTATGCGTACCAGATA
39559192 GCTTTGGCTA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (100 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCGCATGTGTAGTACC
AAGTGCAGGATACTATGCGTACCAGATAACTTCGA
Found at i:39568364 original size:27 final size:28
Alignment explanation
Indices: 39568318--39568371 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
39568308 ACATTGGAGA
*
39568318 AAAATAGTTATCTTACCATATA-AGGGT
1 AAAATAGTCATCTTACCATATATAGGGT
* *
39568345 AAAATAGTCATTTTATCATATATAGGG
1 AAAATAGTCATCTTACCATATATAGGG
39568372 GGTCTAGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (28 bp):
AAAATAGTCATCTTACCATATATAGGGT
Found at i:39573418 original size:40 final size:41
Alignment explanation
Indices: 39573333--39573430 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 41
39573323 CTATTTGTGG
* *
39573333 CACTTAGTGTGCGAGATCGAGATAGCGTCAGCTATATATGG
1 CACTTAGTGTGCGAGATCGAGATAGCGTCAGCTATATACGA
* * * * *
39573374 CACTTAGTGTGCGA-TTTGAGATAGCTTCAGGTATGTACGA
1 CACTTAGTGTGCGAGATCGAGATAGCGTCAGCTATATACGA
* *
39573414 CACTTAATGTGTGAGAT
1 CACTTAGTGTGCGAGAT
39573431 ATCGAGTATG
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
40 31 0.67
41 15 0.33
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (41 bp):
CACTTAGTGTGCGAGATCGAGATAGCGTCAGCTATATACGA
Found at i:39573454 original size:28 final size:28
Alignment explanation
Indices: 39573414--39573467 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
39573404 GTATGTACGA
*
39573414 CACTTAATGTGTGAGATATCGAGTATGG
1 CACTTAATGTGTGAGACATCGAGTATGG
* *
39573442 CACTTAGTGTGTGAGACATTGAGTAT
1 CACTTAATGTGTGAGACATCGAGTAT
39573468 TTAACGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (28 bp):
CACTTAATGTGTGAGACATCGAGTATGG
Found at i:39575050 original size:22 final size:22
Alignment explanation
Indices: 39575022--39575191 Score: 77
Period size: 22 Copynumber: 7.3 Consensus size: 22
39575012 TTCCACGTTC
*
39575022 ATCACATTGGCCATTCTGCCTT
1 ATCACATTGGCCATTCGGCCTT
*
39575044 ATCACATATATG-CA-T-GGTCACATT
1 ATCACAT-T-GGCCATTCGG-C-C-TT
39575068 TATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* *
39575091 ATCACATATGTG-CATGTTC-ACATT
1 ATCACAT-TG-GCCA--TTCGGCCTT
39575115 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* *
39575138 ATCACACATAT-G-CATGTTC-ACATT
1 AT--CACAT-TGGCCA--TTCGGCCTT
39575162 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
39575185 ATCACAT
1 ATCACAT
39575192 ATATGCATGT
Statistics
Matches: 112, Mismatches: 11, Indels: 50
0.65 0.06 0.29
Matches are distributed among these distances:
21 1 0.01
22 32 0.29
23 26 0.23
24 26 0.23
25 25 0.22
26 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:39575073 original size:47 final size:47
Alignment explanation
Indices: 39575019--39575264 Score: 420
Period size: 47 Copynumber: 5.2 Consensus size: 47
39575009 CACTTCCACG
* *
39575019 TTCATCACATTGGCCATTCTGCCTTATCACATATATGCATGGTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
39575066 TTTATCACATTGGCCATTCGGCCTTATCACATATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
39575113 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
39575160 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCAAA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
39575207 TTCATCACATTGGCCATTCGGCCTTATCACATATGTACATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
39575254 TTCATCACATT
1 TTCATCACATT
39575265 AAATCCTAAA
Statistics
Matches: 187, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 187 1.00
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:39577580 original size:13 final size:13
Alignment explanation
Indices: 39577562--39577587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39577552 ATTTTTATTT
39577562 TTAACATAAAATA
1 TTAACATAAAATA
39577575 TTAACATAAAATA
1 TTAACATAAAATA
39577588 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:39579134 original size:28 final size:28
Alignment explanation
Indices: 39579103--39579259 Score: 145
Period size: 28 Copynumber: 5.5 Consensus size: 28
39579093 CTGACTGATT
*
39579103 TCGCACACATAGCGCTCGATTAAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
* * *
39579131 TCGCACACATAGTGCCTCAATTACCA-ATC
1 TCGCACACATAGTG-CTCGATTA-AAGAAC
*
39579160 TCGCACACATAGTGCTCGATTGAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
* * ** *
39579188 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTG-CTCGATTAAAGAAC
* * *
39579217 TGGCACACATAGTGCTCGGTTGAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
* *
39579245 TTGCACACACAGTGC
1 TCGCACACATAGTGC
39579260 CTCATGATTC
Statistics
Matches: 101, Mismatches: 24, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
27 1 0.01
28 55 0.54
29 44 0.44
30 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (28 bp):
TCGCACACATAGTGCTCGATTAAAGAAC
Found at i:39579163 original size:29 final size:29
Alignment explanation
Indices: 39579130--39579231 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
39579120 GATTAAAGAA
39579130 CTCGCACACATAGTGCCTCAATTACCAAT
1 CTCGCACACATAGTGCCTCAATTACCAAT
* **
39579159 CTCGCACACATAGTG-CTCGATTGAAGAA-
1 CTCGCACACATAGTGCCTCAATT-ACCAAT
* **
39579187 CTCGCACACATAGTGCCTCAACTACTGAT
1 CTCGCACACATAGTGCCTCAATTACCAAT
*
39579216 CTGGCACACATAGTGC
1 CTCGCACACATAGTGC
39579232 TCGGTTGAAG
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
28 23 0.38
29 38 0.62
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCAATTACCAAT
Found at i:39579170 original size:57 final size:57
Alignment explanation
Indices: 39579103--39579263 Score: 241
Period size: 57 Copynumber: 2.8 Consensus size: 57
39579093 CTGACTGATT
* * *
39579103 TCGCACACATAGCGCTCGATTAAAGAACTCGCACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
**
39579160 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
* * * *
39579217 TGGCACACATAGTGCTCGGTTGAAGAACTTGCACACACAGTGCCTCA
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCA
39579264 TGATTCTAGC
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 95 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (57 bp):
TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
Found at i:39579344 original size:40 final size:40
Alignment explanation
Indices: 39579269--39580025 Score: 1162
Period size: 40 Copynumber: 18.9 Consensus size: 40
39579259 CCTCATGATT
* *
39579269 CTAGCACGAATGC-CTTCGAGG-TTTAGCCCAGATATATCA
1 CTAGCACGAATGCTCTTCG-GGACTTAGCCCGGATATATCA
*
39579308 CTAGCACGAATGCTCTTTGGGACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
* **
39579348 CTAGCACGAATGCTTTTCGGGACTTAGCCCGGATACGTCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
* ** *
39579388 CTAGCACGAATGCTTTTCGGGACTTAGCCCAAATACATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
* *
39579428 TTAGCACGAATGCTCTTCGGGACTTAGCCCAGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
* * *
39579468 CCAGCACGAATGCTCATCGAGACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
39579508 CTAGCACGAATGCTCTTCGGGACTTAGCCCAGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
* * * * *
39579548 CCAGCACGAATGCTTTTCAGGACTTAGACCGGATACATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
39579588 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
* * *
39579628 CCAGCACGAATGCTCTTCGGGACTTAGCCTGGATACATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
39579668 CTAGCACGAAATGCTCTTCGGGACTTAGCCCGAATATATCA
1 CTAGCACG-AATGCTCTTCGGGACTTAGCCCGGATATATCA
*
39579709 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
39579749 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
39579789 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCAA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATC-A
*
39579830 C-AGCACGAATGCTCTTTGGGACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
39579869 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
39579909 CTAAG-ACTAATGCTCTTCGGGACTTAGCCCGGATATATCA
1 CT-AGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
39579949 CCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
*
39579989 CTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATA
1 CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
39580026 ACATACTGAA
Statistics
Matches: 661, Mismatches: 50, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
39 19 0.03
40 602 0.91
41 40 0.06
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCA
Found at i:39581515 original size:47 final size:47
Alignment explanation
Indices: 39581461--39581700 Score: 412
Period size: 47 Copynumber: 5.1 Consensus size: 47
39581451 CACTTCTACG
*
39581461 TTCATCACATTGGCCATTCTGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
39581508 TTTATCACATTGGCCATTCGGCCTTATCAC--ATGTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
*
39581553 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
39581600 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* *
39581647 TTCATCACATTGGCCATTCGGCCTTATCACATATGTACATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
39581694 TTCATCA
1 TTCATCA
39581701 GATTAAATCC
Statistics
Matches: 183, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
45 43 0.23
47 140 0.77
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Done.